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Wu Z, Takigawa H, Maruyama H, Nambu T, Mashimo C, Okinaga T. TLR2-dependent and independent pyroptosis in dTHP-1 cells induced by Actinomyces oris MG-1. Biochem Biophys Rep 2024; 38:101680. [PMID: 38455593 PMCID: PMC10918485 DOI: 10.1016/j.bbrep.2024.101680] [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: 12/21/2023] [Revised: 02/20/2024] [Accepted: 02/29/2024] [Indexed: 03/09/2024] Open
Abstract
In the immune system, the detection of pathogens through various mechanisms triggers immune responses. Several types of specific programmed cell deaths play a role in the inflammatory reaction. This study emphasizes the inflammatory response induced by Actinomycetes. Actinomyces spp. are resident bacteria in human oral plaque and often serve as a bridge for pathogenic bacteria, which lack affinity to the tooth surface, aiding their colonization of the plaque. We aim to investigate the potential role of Actinomyces oris in the early stages of oral diseases from a new perspective. Actinomyces oris MG-1 (A. oris) was chosen for this research. Differentiated THP-1 (dTHP-1) cells were transiently treated with A. oris to model the inflammatory reaction. Cell viability, as well as relative gene and protein expression levels of dTHP-1 cells, were assessed using CCK-8, quantitative real-time polymerase chain reaction (RT-qPCR), enzyme-linked immunosorbent assay (ELISA), and Western blot assay. The treatment decreased cell viability and increased the expression of inflammatory genes such as IL-1R1 and NLRP3. It was also observed to significantly enhance the release of IL-1β/IL-18 into the supernatant. Immunoblot analysis revealed a notable increase in the expression of N-gasdermin D persisting up to 24 h. Conversely, in models pre-treated with TLR2 inhibitors, N-gasdermin D was detectable only 12 h post-treatment and absent at 24 h. These results suggest that Actinomyces oris MG-1 induces pyroptosis in dTHP-1 cells via TLR2, but the process is not solely dependent on TLR2.
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Affiliation(s)
- Zixin Wu
- Department of Bacteriology, Graduate School of Dentistry, Osaka Dental University, 8-1, Kuzuha-Hanazono, Hirakata, Osaka, 573-1121, Japan
| | - Hiroki Takigawa
- Department of Bacteriology, Osaka Dental University, 8-1, Kuzuha-Hanazono, Hirakata, Osaka, 573-1121, Japan
| | - Hugo Maruyama
- Department of Bacteriology, Osaka Dental University, 8-1, Kuzuha-Hanazono, Hirakata, Osaka, 573-1121, Japan
| | - Takayuki Nambu
- Department of Bacteriology, Osaka Dental University, 8-1, Kuzuha-Hanazono, Hirakata, Osaka, 573-1121, Japan
| | - Chiho Mashimo
- Department of Bacteriology, Osaka Dental University, 8-1, Kuzuha-Hanazono, Hirakata, Osaka, 573-1121, Japan
| | - Toshinori Okinaga
- Department of Bacteriology, Osaka Dental University, 8-1, Kuzuha-Hanazono, Hirakata, Osaka, 573-1121, Japan
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Williams TJ, Allen MA, Ray AE, Benaud N, Chelliah DS, Albanese D, Donati C, Selbmann L, Coleine C, Ferrari BC. Novel endolithic bacteria of phylum Chloroflexota reveal a myriad of potential survival strategies in the Antarctic desert. Appl Environ Microbiol 2024; 90:e0226423. [PMID: 38372512 PMCID: PMC10952385 DOI: 10.1128/aem.02264-23] [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: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 02/20/2024] Open
Abstract
The ice-free McMurdo Dry Valleys of Antarctica are dominated by nutrient-poor mineral soil and rocky outcrops. The principal habitat for microorganisms is within rocks (endolithic). In this environment, microorganisms are provided with protection against sub-zero temperatures, rapid thermal fluctuations, extreme dryness, and ultraviolet and solar radiation. Endolithic communities include lichen, algae, fungi, and a diverse array of bacteria. Chloroflexota is among the most abundant bacterial phyla present in these communities. Among the Chloroflexota are four novel classes of bacteria, here named Candidatus Spiritibacteria class. nov. (=UBA5177), Candidatus Martimicrobia class. nov. (=UBA4733), Candidatus Tarhunnaeia class. nov. (=UBA6077), and Candidatus Uliximicrobia class. nov. (=UBA2235). We retrieved 17 high-quality metagenome-assembled genomes (MAGs) that represent these four classes. Based on genome predictions, all these bacteria are inferred to be aerobic heterotrophs that encode enzymes for the catabolism of diverse sugars. These and other organic substrates are likely derived from lichen, algae, and fungi, as metabolites (including photosynthate), cell wall components, and extracellular matrix components. The majority of MAGs encode the capacity for trace gas oxidation using high-affinity uptake hydrogenases, which could provide energy and metabolic water required for survival and persistence. Furthermore, some MAGs encode the capacity to couple the energy generated from H2 and CO oxidation to support carbon fixation (atmospheric chemosynthesis). All encode mechanisms for the detoxification and efflux of heavy metals. Certain MAGs encode features that indicate possible interactions with other organisms, such as Tc-type toxin complexes, hemolysins, and macroglobulins.IMPORTANCEThe ice-free McMurdo Dry Valleys of Antarctica are the coldest and most hyperarid desert on Earth. It is, therefore, the closest analog to the surface of the planet Mars. Bacteria and other microorganisms survive by inhabiting airspaces within rocks (endolithic). We identify four novel classes of phylum Chloroflexota, and, based on interrogation of 17 metagenome-assembled genomes, we predict specific metabolic and physiological adaptations that facilitate the survival of these bacteria in this harsh environment-including oxidation of trace gases and the utilization of nutrients (including sugars) derived from lichen, algae, and fungi. We propose that such adaptations allow these endolithic bacteria to eke out an existence in this cold and extremely dry habitat.
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Affiliation(s)
- Timothy J. Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Michelle A. Allen
- School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Angelique E. Ray
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Nicole Benaud
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Devan S. Chelliah
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Davide Albanese
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Claudio Donati
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università, Viterbo, Italy
- Mycological Section, Italian Antarctic National Museum (MNA), Genova, Italy
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università, Viterbo, Italy
| | - Belinda C. Ferrari
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
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Rizzo C, Arcadi E, Calogero R, Ciro Rappazzo A, Caruso G, Maimone G, Lo Giudice A, Romeo T, Andaloro F. Deciphering the evolvement of microbial communities from hydrothermal vent sediments in a global change perspective. ENVIRONMENTAL RESEARCH 2024; 240:117514. [PMID: 37890823 DOI: 10.1016/j.envres.2023.117514] [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: 10/17/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023]
Abstract
Microbial communities first respond to changes of external environmental conditions. Observing the microbial responses to environmental changes in terms of taxonomic and functional biodiversity is therefore of great interest, particularly in extreme environments, where the already extreme conditions can become even harsher. In this study, sediment samples from three different shallow hydrothermal vents in Levante Bay (Vulcano Island, Aeolian Islands, Italy) were used to set up microcosm experiments with the aim to explore the microbial dynamics under changing conditions of pH and redox potential over a 90-days period. The leading hypothesis was to establish under microcosm conditions whether the starting microbial communities of the sediments evolved differently depending on their origin. To profile the dynamics of microbial populations over time, biodiversity, enzymatic profile, total cell abundance estimations, total/respiring cell ratio were estimated by using different approaches. An evident change in the microbial community structure was observed, mainly in the microcosm containing the sediment from the most acidified site, which was characterized by a highly diversified microbial community (in prevalence composed of Thermotoga, Desulfobacterota, Planctomycetota, Synergistota and Deferribacterota). An increase in microbial resistant forms (e.g., spore-forming species) with anaerobic metabolism was detected in all experimental conditions. Differential physiological responses characterized the sedimentary microbial communities. Proteolytic activity appeared to be stimulated under microcosm conditions, whereas the alkaline phosphatase activity was significantly depressed at low pH values, like those that were measured at the station showing intermediate pH-conditions. The results confirmed a differential response of microbial communities depending on the starting environmental conditions.
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Affiliation(s)
- Carmen Rizzo
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn-, Sicily Marine Centre, Villa Pace, Contrada Porticatello 29, 98167, Messina, Italy; Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122, Messina, Italy.
| | - Erika Arcadi
- StazioneZoologica Anton Dohrn, Sicily Marine Centre, Department of Biology and Evolution of Marine Organisms, Villa Pace, Contrada Porticatello 29, 98167, Messina, Italy.
| | - Rosario Calogero
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Contrada Porticatello, 29, 98167 Messina, Italy
| | - Alessandro Ciro Rappazzo
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122, Messina, Italy; Campus Scientifico, Ca' Foscari University of Venice, Italy
| | - Gabriella Caruso
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122, Messina, Italy
| | - Giovanna Maimone
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122, Messina, Italy
| | - Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122, Messina, Italy
| | - Teresa Romeo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Contrada Porticatello, 29, 98167, Messina, Italy; National Institute for Environmental Protection and Research, Via Dei Mille 46, 98057, Milazzo, Italy
| | - Franco Andaloro
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Lungomare Cristoforo Colombo, 4521 Palermo, Italy
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Granados-Tristán AL, Hernández-Luna CE, González-Escalante LA, Camacho-Moll ME, Silva-Ramírez B, Bermúdez de León M, Peñuelas-Urquides K. ESX-3 secretion system in Mycobacterium: An overview. Biochimie 2024; 216:46-55. [PMID: 37879428 DOI: 10.1016/j.biochi.2023.10.013] [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: 04/17/2023] [Revised: 09/26/2023] [Accepted: 10/22/2023] [Indexed: 10/27/2023]
Abstract
Mycobacteria are microorganisms distributed in the environment worldwide, and some of them, such as Mycobacterium tuberculosis or M. leprae, are pathogenic. The hydrophobic mycobacterial cell envelope has low permeation and bacteria need to export products across their structure. Mycobacteria possess specialized protein secretion systems, such as the Early Secretory Antigenic Target 6 secretion (ESX) system. Five ESX loci have been described in M. tuberculosis, called ESX-1 to ESX-5. The ESX-3 secretion system has been associated with mycobacterial metabolism and growth. The locus of this system is highly conserved across mycobacterial species. Metallo-proteins regulate negative ESX-3 transcription in high conditions of iron and zinc. Moreover, this secretion system is part of an antioxidant regulatory pathway linked to Zinc. EccA3, EccB3, EccC3, EccD3, and EccE3 are components of the ESX-3 secretion machinery, whereas EsxG-EsxH, PE5-PPE4, and PE15-PPE20 are proteins secreted by this system. In addition, EspG3 and MycP3 are complementary proteins involved in transport and proteolysis respectively. This system is associated to mycobacterial virulence by releasing the bacteria from the phagosome and inhibiting endomembrane damage response. Furthermore, components of this system inhibit the host immune response by reducing the recognition of M. tuberculosis-infected cells. The components of the ESX-3 secretion system play a role in drug resistance and cell wall integrity. Moreover, the expression data of this system indicated that external and internal factors affect ESX-3 locus expression. This review provides an overview of new findings on the ESX-3 secretion system, its regulation, expression, and functions.
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Affiliation(s)
- Ana Laura Granados-Tristán
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico; Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, 66455, Nuevo León, Mexico.
| | - Carlos Eduardo Hernández-Luna
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, 66455, Nuevo León, Mexico.
| | - Laura Adiene González-Escalante
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
| | - María Elena Camacho-Moll
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
| | - Beatriz Silva-Ramírez
- Departamento de Inmunogenética, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
| | - Mario Bermúdez de León
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
| | - Katia Peñuelas-Urquides
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
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Gondhalekar R, Kempes CP, McGlynn SE. Scaling of Protein Function across the Tree of Life. Genome Biol Evol 2023; 15:evad214. [PMID: 38007693 PMCID: PMC10715193 DOI: 10.1093/gbe/evad214] [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: 03/27/2023] [Revised: 11/07/2023] [Accepted: 11/12/2023] [Indexed: 11/28/2023] Open
Abstract
Scaling laws are a powerful way to compare genomes because they put all organisms onto a single curve and reveal nontrivial generalities as genomes change in size. The abundance of functional categories across genomes has previously been found to show power law scaling with respect to the total number of functional categories, suggesting that universal constraints shape genomic category abundance. Here, we look across the tree of life to understand how genome evolution may be related to functional scaling. We revisit previous observations of functional genome scaling with an expanded taxonomy by analyzing 3,726 bacterial, 220 archaeal, and 79 unicellular eukaryotic genomes. We find that for some functional classes, scaling is best described by multiple exponents, revealing previously unobserved shifts in scaling as genome-encoded protein annotations increase or decrease. Furthermore, we find that scaling varies between phyletic groups at both the domain and phyla levels and is less universal than previously thought. This variability in functional scaling is not related to taxonomic phylogeny resolved at the phyla level, suggesting that differences in cell plan or physiology outweigh broad patterns of taxonomic evolution. Since genomes are maintained and replicated by the functional proteins encoded by them, these results point to functional degeneracy between taxonomic groups and unique evolutionary trajectories toward these. We also find that individual phyla frequently span scaling exponents of functional classes, revealing that individual clades can move across scaling exponents. Together, our results reveal unique shifts in functions across the tree of life and highlight that as genomes grow or shrink, proteins of various functions may be added or lost.
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Affiliation(s)
- Riddhi Gondhalekar
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- School of Life Sciences and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | | | - Shawn Erin McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- School of Life Sciences and Technology, Tokyo Institute of Technology, Tokyo, Japan
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Center for Sustainable Resource Science, RIKEN, Saitama, Japan
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Li J, Liu H, Zhao C, Zhang J, He W. Autoinducer-2 quorum sensing regulates biofilm formation and chain elongation metabolic pathways to enhance caproate synthesis in microbial electrochemical system. CHEMOSPHERE 2023; 344:140384. [PMID: 37806331 DOI: 10.1016/j.chemosphere.2023.140384] [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: 05/16/2023] [Revised: 08/26/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023]
Abstract
Quorum sensing (QS) have been explored extensively. However, most studies focused on N-acyl homoserine lactones (AHLs) participating in intraspecies QS. In this study, autoinducer-2 (AI-2, participating in interspecies QS) with different concentration was investigated for chain elongation in microbial electrosynthesis (MES). The results demonstrated that the R3 treatment, which involved adding 10 μM of 4,5-dihydroxy-2,3-pentanedione (DPD) in the reactor, exhibited the best performance. The concentration of caproate was increased by 66.88% and the redox activity of cathodic electroactive biofilms (EABs) was enhanced. Meanwhile, microbial community data indicated that Negativicutes relative abundance was increased obviously in R3 treatment. In this study, the transcriptome Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases were used to analyze the metabolic pathway of chain elongation involving fatty acid biosynthesis (FAB) pathway and reverse β-oxidization (RBO) pathway. KEGG analysis revealed that fatty acid elongation metabolism (p < 0.001), tryptophan metabolism (p < 0.01), arginine and proline metabolism (p < 0.05) were significantly improved in R3 treatment. GO analysis suggested that R3 treatment mainly upregulated significantly transmembrane signaling receptor activity (p < 0.01), oxidoreductase activity (p < 0.05), and phosphorelay signal transduction (p < 0.05). Moreover, metatranscriptomic analyses also showed that R3 treatment could upregulate the LuxP extracellular receptor, LuxO transcriptional activator, LsrB periplasmic protein, and were beneficial to both FAB and RBO pathways. These findings provided a new insight into chain elongation in MES system.
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Affiliation(s)
- Jing Li
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi, 214122, Jiangsu Province, PR China
| | - He Liu
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi, 214122, Jiangsu Province, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou, 215011, Jiangsu Province, PR China.
| | - Chao Zhao
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi, 214122, Jiangsu Province, PR China
| | - Jie Zhang
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi, 214122, Jiangsu Province, PR China
| | - Wanying He
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi, 214122, Jiangsu Province, PR China
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7
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Kawaguchi M, Shimada H, Bessho Y, Nemoto N. Profiling of lipids in Thermus thermophilus HB8 grown under various conditions. J GEN APPL MICROBIOL 2023; 69:79-90. [PMID: 37394432 DOI: 10.2323/jgam.2023.06.006] [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] [Indexed: 07/04/2023]
Abstract
The membrane lipids of Thermus species have unique structures. Only four polar lipid species have so far been identified in Thermus thermophilus HB8; namely, are two phosphoglycolipids and two glycolipids, both of which have three branched fatty acid chains. Other lipid molecules may be present; however, they have not been identified so far. To clarify the whole lipid profile of T. thermophilus HB8, we cultured this organism under four different growth (temperature and/or nutrition) conditions and analyzed the compositions of polar lipids and fatty acids by high-performance thin-layer chromatography (HPTLC) and gas chromatograph-mass spectrometry (GCーMS), respectively. Thirty-one lipid spots were detected on HPTLC plates and profiled in terms of the presence or absence of phosphate, amino, and sugar groups. Then, we allocated ID numbers to all the spots. Comparative analyses of these polar lipids showed that the diversity of lipid molecules increased under high temperature and minimal medium conditions. In particular, aminolipid species increased under high temperature conditions. As for the fatty acid comparison by GC-MS, iso-branched even-numbered carbon atoms, which are unusual in this organism, significantly increased under the minimal medium condition, suggesting that kinds of branched amino acids at the fatty acid terminus varies under different nutrition conditions. In this study, several unidentified lipids were detected, and elucidation of the lipid structures will provide important information on the environmental adaptation of bacteria.
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Affiliation(s)
| | - Haruo Shimada
- BioChromato, Inc
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Yoshitaka Bessho
- RIKEN SPring-8 Center, Harima Institute
- Center for Interdisciplinary AI and Data Science, Ochanomizu University
| | - Naoki Nemoto
- Faculty of Advanced Engineering, Chiba Institute of Technology
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Wiegand S, Sobol M, Schnepp-Pesch LK, Yan G, Iqbal S, Vollmers J, Müller JA, Kaster AK. Taxonomic Re-Classification and Expansion of the Phylum Chloroflexota Based on over 5000 Genomes and Metagenome-Assembled Genomes. Microorganisms 2023; 11:2612. [PMID: 37894270 PMCID: PMC10608941 DOI: 10.3390/microorganisms11102612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
The phylum Chloroflexota (formerly Chloroflexi) encompasses metabolically diverse bacteria that often have high prevalence in terrestrial and aquatic habitats, some even with biotechnological application. However, there is substantial disagreement in public databases which lineage should be considered a member of the phylum and at what taxonomic level. Here, we addressed these issues through extensive phylogenomic analyses. The analyses were based on a collection of >5000 Chloroflexota genomes and metagenome-assembled genomes (MAGs) from public databases, novel environmental sites, as well as newly generated MAGs from publicly available sequence reads via an improved binning approach incorporating covariance information. Based on calculated relative evolutionary divergence, we propose that Candidatus Dormibacterota should be listed as a class (i.e., Ca. Dormibacteria) within Chloroflexota together with the classes Anaerolineae, Chloroflexia, Dehalococcoidia, Ktedonobacteria, Ca. Limnocylindria, Thermomicrobia, and two other classes containing only uncultured members. All other Chloroflexota lineages previously listed at the class rank appear to be rather orders or families in the Anaerolineae and Dehalococcoidia, which contain the vast majority of genomes and exhibited the strongest phylogenetic radiation within the phylum. Furthermore, the study suggests that a common ecophysiological capability of members of the phylum is to successfully cope with low energy fluxes.
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Affiliation(s)
| | | | | | | | | | | | | | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IBG 5), Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany; (S.W.); (M.S.); (L.K.S.-P.); (G.Y.); (S.I.); (J.V.); (J.A.M.)
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9
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Sabnis A, Edwards AM. Lipopolysaccharide as an antibiotic target. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119507. [PMID: 37268022 DOI: 10.1016/j.bbamcr.2023.119507] [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: 04/04/2022] [Revised: 04/18/2023] [Accepted: 05/14/2023] [Indexed: 06/04/2023]
Abstract
Gram-negative bacteria, including Escherichia coli, Pseudomonas aeruginosa and Acinetobacter baumannii are amongst the highest priority drug-resistant pathogens, for which new antibiotics are urgently needed. Whilst antibiotic drug development is inherently challenging, this is particularly true for Gram-negative bacteria due to the presence of the outer membrane, a highly selective permeability barrier that prevents the ingress of several classes of antibiotic. This selectivity is largely due to an outer leaflet composed of the glycolipid lipopolysaccharide (LPS), which is essential for the viability of almost all Gram-negative bacteria. This essentiality, coupled with the conservation of the synthetic pathway across species and recent breakthroughs in our understanding of transport and membrane homeostasis has made LPS an attractive target for novel antibiotic drug development. Several different targets have been explored and small molecules developed that show promising activity in vitro. However, these endeavours have met limited success in clinical testing and the polymyxins, discovered more than 70 years ago, remain the only LPS-targeting drugs to enter the clinic thus far. In this review, we will discuss efforts to develop therapeutic inhibitors of LPS synthesis and transport and the reasons for limited success, and explore new developments in understanding polymyxin mode of action and the identification of new analogues with reduced toxicity and enhanced activity.
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Affiliation(s)
- Akshay Sabnis
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Rd, London SW7 2AZ, UK
| | - Andrew M Edwards
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Rd, London SW7 2AZ, UK.
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Lim Y, Seo JH, Giovannoni SJ, Kang I, Cho JC. Cultivation of marine bacteria of the SAR202 clade. Nat Commun 2023; 14:5098. [PMID: 37607927 PMCID: PMC10444878 DOI: 10.1038/s41467-023-40726-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023] Open
Abstract
Bacteria of the SAR202 clade, within the phylum Chloroflexota, are ubiquitously distributed in the ocean but have not yet been cultivated in the lab. It has been proposed that ancient expansions of catabolic enzyme paralogs broadened the spectrum of organic compounds that SAR202 bacteria could oxidize, leading to transformations of the Earth's carbon cycle. Here, we report the successful cultivation of SAR202 bacteria from surface seawater using dilution-to-extinction culturing. The growth of these strains is very slow (0.18-0.24 day-1) and is inhibited by exposure to light. The genomes, of ca. 3.08 Mbp, encode archaella (archaeal motility structures) and multiple sets of enzyme paralogs, including 80 genes coding for enolase superfamily enzymes and 44 genes encoding NAD(P)-dependent dehydrogenases. We propose that these enzyme paralogs participate in multiple parallel pathways for non-phosphorylative catabolism of sugars and sugar acids. Indeed, we demonstrate that SAR202 strains can utilize several substrates that are metabolized through the predicted pathways, such as sugars ʟ-fucose and ʟ-rhamnose, as well as their lactone and acid forms.
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Affiliation(s)
- Yeonjung Lim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
- Center for Molecular and Cell Biology, Inha University, Incheon, 22212, Republic of Korea
| | - Ji-Hui Seo
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | | | - Ilnam Kang
- Center for Molecular and Cell Biology, Inha University, Incheon, 22212, Republic of Korea.
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea.
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11
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Sarrami Z, Sedghi M, Mohammadi I, Bedford M, Miranzadeh H, Ghasemi R. Effects of bacteriophage on Salmonella Enteritidis infection in broilers. Sci Rep 2023; 13:12198. [PMID: 37500690 PMCID: PMC10374914 DOI: 10.1038/s41598-023-38791-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
Bacteriophages (BP) are viruses that can infect bacteria. The present study evaluated the effect of BP on Salmonella infected broilers. A number of 150 day-old broilers were used in a completely randomized design with five treatments that included: (1) basal diet from day 0 to 28; (2) basal diet + 0.3 g/kg of colistin from day 0 to 28; (3) basal diet from day 1 to 13, and basal diet + 0.4 g/kg of colistin from day 14 to 28; (4) basal diet + 1 g/kg of BP from day 0 to 28; (5) basal diet + 1.5 g/kg of BP from day 0 to 28. On day 13, 15 chickens from each treatment were challenged by Salmonella Enteritidis (SE), while fifteen from each treatment were not; instead, they were kept in the same cage with the challenged chickens (exposed chickens). At 7 and 14 days post-challenge, the number of SE and coliform bacteria in the cecum and liver of colistin and BP-fed birds was lower than the control treatment. In exposed and challenged chickens, the height and surface area of villus were greater in the BP and colistin-supplemented groups. Serum concentrations of aspartate aminotransferase and alanine transaminase were greater, while serum albumin and triglycerides concentrations were lower in the control treatment. The liver of the challenged chickens had more pathological lesions than exposed birds. BP significantly decreased PPARγ gene expression in exposed chickens. In the challenged and exposed chickens, TLR4 gene expression was lower in BP and colistin-treated birds as compared to the control. In conclusion, adding BP to the diet from the day of age prevents the spread of Salmonella.
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Affiliation(s)
- Zahra Sarrami
- Department of Animal Sciences, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | - Mohammad Sedghi
- Department of Animal Sciences, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
| | - Ishmael Mohammadi
- Department of Animal Sciences, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | | | - Hadi Miranzadeh
- Department of Animal Sciences, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | - Razie Ghasemi
- Department of Animal Sciences, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
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12
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Dhakephalkar T, Stukey G, Guan Z, Carman GM, Klein EA. Characterization of an evolutionarily distinct bacterial ceramide kinase from Caulobacter crescentus. J Biol Chem 2023:104894. [PMID: 37286040 PMCID: PMC10331486 DOI: 10.1016/j.jbc.2023.104894] [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: 05/02/2023] [Revised: 05/27/2023] [Accepted: 06/01/2023] [Indexed: 06/09/2023] Open
Abstract
A common feature among nearly all Gram-negative bacteria is the requirement for lipopolysaccharide (LPS) in the outer leaflet of the outer membrane. LPS provides structural integrity to the bacterial membrane which aids bacteria in maintaining their shape and acts as a barrier from environmental stress and harmful substances such as detergents and antibiotics. Recent work has demonstrated that Caulobacter crescentus can survive without LPS due to the presence of the anionic sphingolipid ceramide-phosphoglycerate. Based on genetic evidence, we predicted that protein CpgB functions as a ceramide kinase and performs the first step in generating the phosphoglycerate head group. Here, we characterized the kinase activity of recombinantly expressed CpgB and demonstrated that it can phosphorylate ceramide to form ceramide 1-phosphate. The pH optimum for CpgB was 7.5, and the enzyme required Mg2+ as a cofactor. Mn2+, but not other divalent cations, could substitute for Mg2+. Under these conditions, the enzyme exhibited typical Michaelis-Menten kinetics with respect to NBD-C6-ceramide (Km,app=19.2 ± 5.5 μM; Vmax,app=2590 ± 230 pmol/min/mg enzyme) and ATP (Km,app=0.29 ± 0.07 mM; Vmax,app=10100 ± 996 pmol/min/mg enzyme). Phylogenetic analysis of CpgB revealed that CpgB belongs to a new class of ceramide kinases which is distinct from its eukaryotic counterpart; furthermore, the pharmacological inhibitor of human ceramide kinase (NVP-231) had no effect on CpgB. The characterization of a new bacterial ceramide kinase opens avenues for understanding the structure and function of the various microbial phosphorylated sphingolipids.
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Affiliation(s)
| | - Geordan Stukey
- Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food Nutrition and Health, Rutgers University, New Brunswick, NJ 08901, USA
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - George M Carman
- Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food Nutrition and Health, Rutgers University, New Brunswick, NJ 08901, USA
| | - Eric A Klein
- Biology Department, Rutgers University-Camden, Camden, NJ 08102, USA; Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food Nutrition and Health, Rutgers University, New Brunswick, NJ 08901, USA; Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ 08102, USA.
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13
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Khomich M, Lin H, Malinovschi A, Brix S, Cestelli L, Peddada S, Johannessen A, Eriksen C, Real FG, Svanes C, Bertelsen RJ. Association between lipid-A-producing oral bacteria of different potency and fractional exhaled nitric oxide in a Norwegian population-based adult cohort. J Transl Med 2023; 21:354. [PMID: 37246224 DOI: 10.1186/s12967-023-04199-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/14/2023] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND Lipid A is the primary immunostimulatory part of the lipopolysaccharide (LPS) molecule. The inflammatory response of LPS varies and depends upon the number of acyl chains and phosphate groups in lipid A which is specific for a bacterial species or strain. Traditional LPS quantification assays cannot distinguish between the acylation degree of lipid A molecules, and therefore little is known about how bacteria with different inflammation-inducing potencies affect fractional exhaled nitric oxide (FeNO). We aimed to explore the association between pro-inflammatory hexa- and less inflammatory penta-acylated LPS-producing oral bacteria and FeNO as a marker of airway inflammation. METHODS We used data from a population-based adult cohort from Norway (n = 477), a study center of the RHINESSA multi-center generation study. We applied statistical methods on the bacterial community- (prediction with MiRKAT) and genus-level (differential abundance analysis with ANCOM-BC) to investigate the association between the oral microbiota composition and FeNO. RESULTS We found the overall composition to be significantly associated with increasing FeNO levels independent of covariate adjustment, and abundances of 27 bacterial genera to differ in individuals with high FeNO vs. low FeNO levels. Hexa- and penta-acylated LPS producers made up 2.4% and 40.8% of the oral bacterial genera, respectively. The Bray-Curtis dissimilarity within hexa- and penta-acylated LPS-producing oral bacteria was associated with increasing FeNO levels independent of covariate adjustment. A few single penta-acylated LPS producers were more abundant in individuals with low FeNO vs. high FeNO, while hexa-acylated LPS producers were found not to be enriched. CONCLUSIONS In a population-based adult cohort, FeNO was observed to be associated with the overall oral bacterial community composition. The effect of hexa- and penta-acylated LPS-producing oral bacteria was overall significant when focusing on Bray-Curtis dissimilarity within each of the two communities and FeNO levels, but only penta-acylated LPS producers appeared to be reduced or absent in individuals with high FeNO. It is likely that the pro-inflammatory effect of hexa-acylated LPS producers is counteracted by the dominance of the more abundant penta-acylated LPS producers in this population-based adult cohort involving mainly healthy individuals.
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Affiliation(s)
- Maryia Khomich
- Department of Clinical Science, University of Bergen, Bergen, Norway.
| | - Huang Lin
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences (NIEHS), NIH, Research Triangle Park, Durham, NC, USA
| | - Andrei Malinovschi
- Department of Medical Sciences, Clinical Physiology, Uppsala University, Uppsala, Sweden
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lucia Cestelli
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Shyamal Peddada
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences (NIEHS), NIH, Research Triangle Park, Durham, NC, USA
| | - Ane Johannessen
- Department of Global Public Health and Primary Care, Center for International Health, University of Bergen, Bergen, Norway
| | - Carsten Eriksen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- Center for Molecular Prediction of Inflammatory Bowel Disease (PREDICT), Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
| | - Francisco Gomez Real
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Cecilie Svanes
- Department of Global Public Health and Primary Care, Center for International Health, University of Bergen, Bergen, Norway
- Department of Occupational Medicine, Haukeland University Hospital, Bergen, Norway
| | - Randi Jacobsen Bertelsen
- Department of Clinical Science, University of Bergen, Bergen, Norway.
- Oral Health Center of Expertise in Western Norway, Bergen, Norway.
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14
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Sexton D, Hashimi A, Beskrovnaya P, Sibanda L, Huan T, Tocheva E. The cell envelope of Thermotogae suggests a mechanism for outer membrane biogenesis. Proc Natl Acad Sci U S A 2023; 120:e2303275120. [PMID: 37094164 PMCID: PMC10160955 DOI: 10.1073/pnas.2303275120] [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: 03/03/2023] [Accepted: 03/29/2023] [Indexed: 04/26/2023] Open
Abstract
The presence of a cell membrane is one of the major structural components defining life. Recent phylogenomic analyses have supported the hypothesis that the last universal common ancestor (LUCA) was likely a diderm. Yet, the mechanisms that guided outer membrane (OM) biogenesis remain unknown. Thermotogae is an early-branching phylum with a unique OM, the toga. Here, we use cryo-electron tomography to characterize the in situ cell envelope architecture of Thermotoga maritima and show that the toga is made of extended sheaths of β-barrel trimers supporting small (~200 nm) membrane patches. Lipidomic analyses identified the same major lipid species in the inner membrane (IM) and toga, including the rare to bacteria membrane-spanning ether-bound diabolic acids (DAs). Proteomic analyses revealed that the toga was composed of multiple SLH-domain containing Ompα and novel β-barrel proteins, and homology searches detected variable conservations of these proteins across the phylum. These results highlight that, in contrast to the SlpA/OmpM superfamily of proteins, Thermotoga possess a highly diverse bipartite OM-tethering system. We discuss the implications of our findings with respect to other early-branching phyla and propose that a toga-like intermediate may have facilitated monoderm-to-diderm cell envelope transitions.
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Affiliation(s)
- Danielle L. Sexton
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver,V6T1Z3 BC, Canada
| | - Ameena Hashimi
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver,V6T1Z3 BC, Canada
| | - Polina Beskrovnaya
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver,V6T1Z3 BC, Canada
| | - Lloyd Sibanda
- Department of Chemistry, University of British Columbia, Vancouver,V6T1Z1 BC, Canada
| | - Tao Huan
- Department of Chemistry, University of British Columbia, Vancouver,V6T1Z1 BC, Canada
| | - Elitza I. Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver,V6T1Z3 BC, Canada
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15
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Dhakephalkar T, Stukey G, Guan Z, Carman GM, Klein EA. Characterization of an evolutionarily distinct bacterial ceramide kinase from Caulobacter crescentus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.01.538943. [PMID: 37205603 PMCID: PMC10187206 DOI: 10.1101/2023.05.01.538943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A common feature among nearly all Gram-negative bacteria is the requirement for lipopolysaccharide (LPS) in the outer leaflet of the outer membrane. LPS provides structural integrity to the bacterial membrane which aids bacteria in maintaining their shape and acts as a barrier from environmental stress and harmful substances such as detergents and antibiotics. Recent work has demonstrated that Caulobacter crescentus can survive without LPS due to the presence of the anionic sphingolipid ceramide-phosphoglycerate. Based on genetic evidence, we predicted that protein CpgB functions as a ceramide kinase and performs the first step in generating the phosphoglycerate head group. Here, we characterized the kinase activity of recombinantly expressed CpgB and demonstrated that it can phosphorylate ceramide to form ceramide 1-phosphate. The pH optimum for CpgB was 7.5, and the enzyme required Mg 2+ as a cofactor. Mn 2+ , but not other divalent cations, could substitute for Mg 2+ . Under these conditions, the enzyme exhibited typical Michaelis-Menten kinetics with respect to NBD-C6-ceramide (K m,app =19.2 ± 5.5 μM; V max,app =2586.29 ± 231.99 pmol/min/mg enzyme) and ATP (K m,app =0.29 ± 0.07 mM; V max,app =10067.57 ± 996.85 pmol/min/mg enzyme). Phylogenetic analysis of CpgB revealed that CpgB belongs to a new class of ceramide kinases which is distinct from its eukaryotic counterpart; furthermore, the pharmacological inhibitor of human ceramide kinase (NVP-231) had no effect on CpgB. The characterization of a new bacterial ceramide kinase opens avenues for understanding the structure and function of the various microbial phosphorylated sphingolipids.
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16
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Zare F, Ghasemi N, Bansal N, Hosano H. Advances in pulsed electric stimuli as a physical method for treating liquid foods. Phys Life Rev 2023; 44:207-266. [PMID: 36791571 DOI: 10.1016/j.plrev.2023.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023]
Abstract
There is a need for alternative technologies that can deliver safe and nutritious foods at lower costs as compared to conventional processes. Pulsed electric field (PEF) technology has been utilised for a plethora of different applications in the life and physical sciences, such as gene/drug delivery in medicine and extraction of bioactive compounds in food science and technology. PEF technology for treating liquid foods involves engineering principles to develop the equipment, and quantitative biochemistry and microbiology techniques to validate the process. There are numerous challenges to address for its application in liquid foods such as the 5-log pathogen reduction target in food safety, maintaining the food quality, and scale up of this physical approach for industrial integration. Here, we present the engineering principles associated with pulsed electric fields, related inactivation models of microorganisms, electroporation and electropermeabilization theory, to increase the quality and safety of liquid foods; including water, milk, beer, wine, fruit juices, cider, and liquid eggs. Ultimately, we discuss the outlook of the field and emphasise research gaps.
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Affiliation(s)
- Farzan Zare
- School of Information Technology and Electrical Engineering, The University of Queensland, Brisbane, St Lucia QLD 4072, Australia; School of Agriculture and Food Sciences, The University of Queensland, St Lucia QLD 4072, Australia
| | - Negareh Ghasemi
- School of Information Technology and Electrical Engineering, The University of Queensland, Brisbane, St Lucia QLD 4072, Australia
| | - Nidhi Bansal
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia QLD 4072, Australia
| | - Hamid Hosano
- Biomaterials and Bioelectrics Department, Institute of Industrial Nanomaterials, Kumamoto University, Kumamoto 860-8555, Japan.
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17
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Paek S, Kawai F, Venisetty N, Kim Y, Yeo HJ. Crystal structure of Campylobacter jejuni lipoprotein Cj1090c. Proteins 2023; 91:293-299. [PMID: 36201627 DOI: 10.1002/prot.26434] [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: 10/13/2021] [Revised: 09/16/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
Abstract
In Gram-negative bacteria, lipopolysaccharide (LPS) is an essential component of the asymmetric outer membrane (OM). LptE is an OM lipoprotein that forms a complex with the β-barrel OM protein, LptD. Incorporation of LPS into the OM outer leaflet is essential for bacterial viability, and mediated by the LptD/E complex. The genome of Campylobacter jejuni, a major foodborne pathogen, contains over 20 putative lipoproteins including Cj1090c. Here, we report the crystal structure of Cj1090c at 2.4 Å resolution, revealing structural evidence for LptE in C. jejuni. The analysis of this crystal structure, along with the genomic context, allows us to propose the C. jejuni LPS transport system for the first time, and permits for discussion of the features of the LptD/E complex of C. jejuni.
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Affiliation(s)
- Seonghee Paek
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States
| | - Fumihiro Kawai
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States
| | - Nilamani Venisetty
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States
| | - Youngchang Kim
- Structural Biology Center, Argonne National Laboratory, Lemont, Illinois, United States
| | - Hye-Jeong Yeo
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States
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18
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Chen JW, Shih CJ, Wu LW, Wu YC, Chiang WF, Chen YL, Wu JH. Phocaeicola oris sp. nov., an anaerobic bacterium isolated from the saliva of a patient with oral squamous cell carcinoma. Int J Syst Evol Microbiol 2023; 73. [PMID: 36749694 DOI: 10.1099/ijsem.0.005703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
A Gram-stain-negative or -positive, strictly anaerobic, non-spore-forming and pleomorphic bacterium (designated 14-104T) was isolated from the saliva sample of a patient with oral squamous cell carcinoma. It was an acid-tolerant neutralophilic mesophile, growing at between 20 and 40 °C (with optimum growth at 30 °C) and pH between pH 3.0 and 7.0 (with optimum growth at pH 6.0-7.0). It contained anteiso-C15 : 0 and C15 : 0 as the major fatty acids. The genome size of strain 14-104T was 2.98 Mbp, and the G+C content was 39.6 mol%. It shared <87 % 16S rRNA sequence similarity, <71 % orthologous average nucleotide identity, <76 % average amino acid identity and <68 %% of conserved proteins with its closest relative, Phocaeicola abscessus CCUG 55929T. Reconstruction of phylogenetic and phylogenomic trees revealed that strain 14-104T and P. abscessus CCUG 55929T were clustered as a distinct clade without any other terminal node. The phylogenetic and phylogenomic analyses along with physiological and chemotaxonomic data indicated that strain 14-104T represents a novel species in the genus Phocaeicola, for which the name Phocaeicola oris sp. nov. is proposed. The type strain is 14-104T (=BCRC 81305T= NBRC 115041T).
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Affiliation(s)
- Jiung-Wen Chen
- Department of Environmental Engineering, National Cheng Kung University, Tainan, Taiwan, ROC.,Present address: Department of Biology, The University of Alabama at Birmingham, 1300 University Blvd, AL 35294, Birmingham, USA
| | - Chao-Jen Shih
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Li-Wha Wu
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC.,Department of Laboratory Science and Technology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, ROC
| | - Yen-Chi Wu
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Wei-Fan Chiang
- Department of Oral & Maxillofacial Surgery, Chi-Mei Medical Center, Liouying, Taiwan, ROC
| | - Yuh-Ling Chen
- Institute of Oral Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Jer-Horng Wu
- Department of Environmental Engineering, National Cheng Kung University, Tainan, Taiwan, ROC
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19
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Xu XJ, Lang JD, Yang J, Long B, Liu XD, Zeng XF, Tian G, You X. Differences of gut microbiota and behavioral symptoms between two subgroups of autistic children based on γδT cells-derived IFN-γ Levels: A preliminary study. Front Immunol 2023; 14:1100816. [PMID: 36875075 PMCID: PMC9975759 DOI: 10.3389/fimmu.2023.1100816] [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: 11/18/2022] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
Background Autism Spectrum Disorders (ASD) are defined as a group of pervasive neurodevelopmental disorders, and the heterogeneity in the symptomology and etiology of ASD has long been recognized. Altered immune function and gut microbiota have been found in ASD populations. Immune dysfunction has been hypothesized to involve in the pathophysiology of a subtype of ASD. Methods A cohort of 105 ASD children were recruited and grouped based on IFN-γ levels derived from ex vivo stimulated γδT cells. Fecal samples were collected and analyzed with a metagenomic approach. Comparison of autistic symptoms and gut microbiota composition was made between subgroups. Enriched KEGG orthologues markers and pathogen-host interactions based on metagenome were also analyzed to reveal the differences in functional features. Results The autistic behavioral symptoms were more severe for children in the IFN-γ-high group, especially in the body and object use, social and self-help, and expressive language performance domains. LEfSe analysis of gut microbiota revealed an overrepresentation of Selenomonadales, Negatiyicutes, Veillonellaceae and Verrucomicrobiaceae and underrepresentation of Bacteroides xylanisolvens and Bifidobacterium longum in children with higher IFN-γ level. Decreased metabolism function of carbohydrate, amino acid and lipid in gut microbiota were found in the IFN-γ-high group. Additional functional profiles analyses revealed significant differences in the abundances of genes encoding carbohydrate-active enzymes between the two groups. And enriched phenotypes related to infection and gastroenteritis and underrepresentation of one gut-brain module associated with histamine degradation were also found in the IFN-γ-High group. Results of multivariate analyses revealed relatively good separation between the two groups. Conclusions Levels of IFN-γ derived from γδT cell could serve as one of the potential candidate biomarkers to subtype ASD individuals to reduce the heterogeneity associated with ASD and produce subgroups which are more likely to share a more similar phenotype and etiology. A better understanding of the associations among immune function, gut microbiota composition and metabolism abnormalities in ASD would facilitate the development of individualized biomedical treatment for this complex neurodevelopmental disorder.
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Affiliation(s)
- Xin-Jie Xu
- Medical Science Research Center, Research Center for Translational Medicine, Department of Scientific Research, Peking Union Medical College Hospital, Beijing, China.,Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ji-Dong Lang
- Precision Medicine Center, Geneis Beijing Co., Ltd., Beijing, China
| | - Jun Yang
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bo Long
- Medical Science Research Center, Research Center for Translational Medicine, Department of Scientific Research, Peking Union Medical College Hospital, Beijing, China
| | - Xu-Dong Liu
- Medical Science Research Center, Research Center for Translational Medicine, Department of Scientific Research, Peking Union Medical College Hospital, Beijing, China
| | - Xiao-Feng Zeng
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Geng Tian
- Precision Medicine Center, Geneis Beijing Co., Ltd., Beijing, China
| | - Xin You
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China.,Autism Special Fund, Peking Union Medical Foundation, Beijing, China
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20
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Sharma U, Rawat D, Mukherjee P, Farooqi F, Mishra V, Sharma RS. Ecological life strategies of microbes in response to antibiotics as a driving factor in soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158791. [PMID: 36108841 DOI: 10.1016/j.scitotenv.2022.158791] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/31/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
Antibiotics as a selection pressure driving the evolution of soil microbial communities is not well understood. Since microbial functions govern ecosystem services, an ecological framework is required to understand and predict antibiotic-induced functional and structural changes in microbial communities. Therefore, metagenomic studies explaining the impacts of antibiotics on soil microbial communities were mined, and alterations in microbial taxa were analyzed through an ecological lens using Grimes's Competitor-Stress tolerator-Ruderal (CSR) model. We propose considering antibiotics as the primary abiotic factor mentioned in the CSR model and classifying non-susceptible microbial taxa as degraders, resistant, and resilient groups analogous to competitors, stress tolerators, and ruderal strategists, respectively. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were among the phyla harboring most members with antibiotic-resistant groups. However, some antibiotic-resistant microbes in these phyla could not only tolerate but also subsist solely on antibiotics, while others degraded antibiotics as a part of secondary metabolism. Irrespective of their taxonomic affiliation, microbes with each life strategy displayed similar phenotypic characteristics. Therefore, it is recommended to consider microbial functional traits associated with each life strategy while analyzing the ecological impacts of antibiotics. Also, potential ecological crises posed by antibiotics through changes in microbial community and ecosystem functions were visualized. Applying ecological theory to understand and predict antibiotics-induced changes in microbial communities will also provide better insight into microbial behavior in the background of emerging contaminants and help develop a robust ecological classification system of microbes.
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Affiliation(s)
- Udita Sharma
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India
| | - Deepak Rawat
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India; Department of Environmental Studies, Janki Devi Memorial College, University of Delhi, Delhi 110060, India
| | - Paromita Mukherjee
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India
| | - Furqan Farooqi
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India
| | - Vandana Mishra
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India; Centre for Interdisciplinary Studies on Mountain & Hill Environment (CISMHE), University of Delhi, Delhi 110007, India.
| | - Radhey Shyam Sharma
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India; Delhi School of Climate Change & Sustainability, Institute of Eminence, University of Delhi, Delhi 110007, India.
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21
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Xu XL, Zhao Y, Chen MM, Li Y, Li Y, Wu SJ, Zhang JL, Zhang XS, Yu K, Lian ZX. Shifts in intestinal microbiota and improvement of sheep immune response to resist Salmonella infection using Toll-like receptor 4 (TLR4) overexpression. Front Microbiol 2023; 14:1075164. [PMID: 36876076 PMCID: PMC9974671 DOI: 10.3389/fmicb.2023.1075164] [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: 10/20/2022] [Accepted: 01/25/2023] [Indexed: 02/17/2023] Open
Abstract
Introduction Toll-like receptor 4 (TLR4) identifies Gram-negative bacteria or their products and plays a crucial role in host defense against invading pathogens. In the intestine, TLR4 recognizes bacterial ligands and interacts with the immune system. Although TLR4 signaling is a vital component of the innate immune system, the influence of TLR4 overexpression on innate immune response and its impact on the composition of the intestinal microbiota is unknown. Methods Here, we obtained macrophages from sheep peripheral blood to examine phagocytosis and clearance of Salmonella Typhimurium (S. Typhimurium) in macrophages. Meanwhile, we characterized the complex microbiota inhabiting the stools of TLR4 transgenic (TG) sheep and wild-type (WT) sheep using 16S ribosomal RNA (rRNA) deep sequencing. Results The results showed that TLR4 overexpression promoted the secretion of more early cytokines by activating downstream signaling pathways after stimulation by S. Typhimurium. Furthermore, diversity analysis demonstrated TLR4 overexpression increased microbial community diversity and regulated the composition of intestinal microbiota. More importantly, TLR4 overexpression adjusted the gut microbiota composition and maintained intestinal health by reducing the ratio of Firmicutes/Bacteroidetes and inflammation and oxidative stress-producing bacteria (Ruminococcaceae, Christensenellaceae) and upregulating the abundance of Bacteroidetes population and short-chain fatty acid (SCFA)-producing bacteria, including Prevotellaceae. These dominant bacterial genera changed by TLR4 overexpression revealed a close correlation with the metabolic pathways of TG sheep. Discussion Taken together, our findings suggested that TLR4 overexpression can counteract S. Typhimurium invasion as well as resist intestinal inflammation in sheep by regulating intestinal microbiota composition and enhancing anti-inflammatory metabolites.
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Affiliation(s)
- Xue-Ling Xu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yue Zhao
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ming-Ming Chen
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yan Li
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yao Li
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Su-Jun Wu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jin-Long Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Tianjin Institute of Animal Sciences, Tianjin, China
| | - Xiao-Sheng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Tianjin Institute of Animal Sciences, Tianjin, China
| | - Kun Yu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zheng-Xing Lian
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Plant-associated fungi support bacterial resilience following water limitation. THE ISME JOURNAL 2022; 16:2752-2762. [PMID: 36085516 PMCID: PMC9666503 DOI: 10.1038/s41396-022-01308-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 08/01/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
Drought disrupts soil microbial activity and many biogeochemical processes. Although plant-associated fungi can support plant performance and nutrient cycling during drought, their effects on nearby drought-exposed soil microbial communities are not well resolved. We used H218O quantitative stable isotope probing (qSIP) and 16S rRNA gene profiling to investigate bacterial community dynamics following water limitation in the hyphospheres of two distinct fungal lineages (Rhizophagus irregularis and Serendipita bescii) grown with the bioenergy model grass Panicum hallii. In uninoculated soil, a history of water limitation resulted in significantly lower bacterial growth potential and growth efficiency, as well as lower diversity in the actively growing bacterial community. In contrast, both fungal lineages had a protective effect on hyphosphere bacterial communities exposed to water limitation: bacterial growth potential, growth efficiency, and the diversity of the actively growing bacterial community were not suppressed by a history of water limitation in soils inoculated with either fungus. Despite their similar effects at the community level, the two fungal lineages did elicit different taxon-specific responses, and bacterial growth potential was greater in R. irregularis compared to S. bescii-inoculated soils. Several of the bacterial taxa that responded positively to fungal inocula belong to lineages that are considered drought susceptible. Overall, H218O qSIP highlighted treatment effects on bacterial community structure that were less pronounced using traditional 16S rRNA gene profiling. Together, these results indicate that fungal-bacterial synergies may support bacterial resilience to moisture limitation.
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23
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Briddon CL, Szekeres E, Hegedüs A, Nicoară M, Chiriac C, Stockenreiter M, Drugă B. The combined impact of low temperatures and shifting phosphorus availability on the competitive ability of cyanobacteria. Sci Rep 2022; 12:16409. [PMID: 36180771 PMCID: PMC9525609 DOI: 10.1038/s41598-022-20580-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
In freshwater systems, cyanobacteria are strong competitors under enhanced temperature and eutrophic conditions. Understanding their adaptive and evolutionary potential to multiple environmental states allows us to accurately predict their response to future conditions. To better understand if the combined impacts of temperature and nutrient limitation could suppress the cyanobacterial blooms, a single strain of Microcystis aeruginosa was inoculated into natural phytoplankton communities with different nutrient conditions: oligotrophic, eutrophic and eutrophic with the addition of bentophos. We found that the use of the bentophos treatment causes significant differences in prokaryotic and eukaryotic communities. This resulted in reduced biodiversity among the eukaryotes and a decline in cyanobacterial abundance suggesting phosphorus limitation had a strong impact on the community structure. The low temperature during the experiment lead to the disappearance of M. aeruginosa in all treatments and gave other phytoplankton groups a competitive advantage leading to the dominance of the eukaryotic families that have diverse morphologies and nutritional modes. These results show cyanobacteria have a reduced competitive advantage under certain temperature and nutrient limiting conditions and therefore, controlling phosphorus concentrations could be a possible mitigation strategy for managing harmful cyanobacterial blooms in a future warmer climate.
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Affiliation(s)
- Charlotte L Briddon
- Institute of Biological Research (NIRDBS), 48 Republicii Street, 400015, Cluj-Napoca, Romania
| | - Edina Szekeres
- Institute of Biological Research (NIRDBS), 48 Republicii Street, 400015, Cluj-Napoca, Romania
| | - Adriana Hegedüs
- Institute of Biological Research (NIRDBS), 48 Republicii Street, 400015, Cluj-Napoca, Romania
| | - Maria Nicoară
- Institute of Biological Research (NIRDBS), 48 Republicii Street, 400015, Cluj-Napoca, Romania
| | - Cecilia Chiriac
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, 37005, České Budějovice, Czech Republic
| | - Maria Stockenreiter
- Department of Biology II, Experimental Aquatic Ecology, Ludwig-Maximilians-Universitӓt Müchen, Groβhaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Bogdan Drugă
- Institute of Biological Research (NIRDBS), 48 Republicii Street, 400015, Cluj-Napoca, Romania.
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24
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Peng W, Talpur MZ, Zeng Y, Xie P, Li J, Wang S, Wang L, Zhu X, Gao P, Jiang Q, Shu G, Zhang H. Influence of fermented feed additive on gut morphology, immune status, and microbiota in broilers. BMC Vet Res 2022; 18:218. [PMID: 35689199 PMCID: PMC9185985 DOI: 10.1186/s12917-022-03322-4] [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: 01/19/2022] [Accepted: 05/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND This study examined the effects of a solid-state fermented feed additive (FFA) on the small intestine histology/morphology, immunity and microbiota of broilers. Two hundred eighty-eight day-old Arbor Acre chicks, were randomly assigned to one of four groups (each group has 6 replicates, with each replicate containing 12 chickens). The negative control (NC; basal diet), the positive control (PC; basal diet +antibiotic 15 ppm), the fermented feed additive low dose (FFL; basal diet + 0.3 kg/t FFA), and the fermented feed additive high dose (FFH; 3 kg/t FFA) with Lactobacillus casei (L.casei). RESULTS The study found that the FFH and FFL groups gained more weight (1-21d) and the FFL and PC diets had better feed conversion ratio (P < 0.05) than the NC from 0-42d. The FFH group had higher villus height (P < 0.05) in the duodenum than the PC and villus height to crypt depth ratio VH/CD compared to PC and FFL groups. The FFL chickens had greater (P < 0.05) jejunal and ileal villus height than PC and NC groups respectively. The FFL group had a higher ileal VH/CD ratio (P < 0.05). Jejunum VH/CD was higher in FFL and FFH (P < 0.05) than PC (P < 0.05). FFH had a smaller thymus than NC (P < 0.05). FFA diets also increased IL-10 expression (P < 0.05). While IL-1 and TLR4 mRNA expression decreased (P < 0.05) compared to NC. The microbiota analysis showed that the microorganisms that have pathogenic properties such as phylum Delsulfobacterota and class Desulfovibriona and Negativicutes was also significantly reduced in the group treated with FFH and PC while microorganisms having beneficial properties like Lactobacillaceae family, Lactobacillus aviarus genus and Lactobacillus spp were also tended to increase in the FFH and FFL fermented feed groups compared to the PC and NC groups. CONCLUSION These findings suggested that the FFA diet may modulate cecal microbiota by reducing pathogenic microorganisms such as phylum Delsulfobacterota and class Desulfovibriona and Negativicutes improve beneficial microorganisms like Lactobacillaceae family, Lactobacillus aviarus genus and Lactobacillus spp. While FFA diet also affect immunity, and gene expression related to immunity.
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Affiliation(s)
- Wentong Peng
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Mir Zulqarnain Talpur
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yuxian Zeng
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Peipei Xie
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jincheng Li
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Songbo Wang
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Lina Wang
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xiaotong Zhu
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Ping Gao
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Qingyan Jiang
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Gang Shu
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China.
| | - Haijun Zhang
- Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
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Rivas-Párraga R, Izquierdo A, Sánchez K, Bolaños-Guerrón D, Alfaro-Núñez A. Identification and phylogenetic characterization based on DNA sequences from RNA ribosomal genes of thermophilic microorganisms in a high elevation Andean tropical geothermal spring. BIONATURA 2022. [DOI: 10.21931/rb/2022.07.02.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Several microorganisms can survive in harsh acid environments in geothermal springs at high temperatures across the Equatorial Andes Mountains. However, little is known about their physiological features and phylogenetic composition. Here we identify thermophilic microorganisms (bacteria, fungi, and microalgae) hosted in an almost unexplored geothermal spring (known as “Aguas Hediondas”). The phylogeny of the cultures was determined by analyzing physiological features and DNA sequences of PCR products for 16S rRNA, ITS, and 23S rRNA genes. Twenty pure cultures were isolated from the samples, including 17 for bacteria, one for cyanobacterium, one for eukaryotic microalgae, and one for fungus. Most bacterial strains were gram-positive, spore-forming, and bacilli (Bacillus). Cyanobacterium strain belonged to Chroococcidiopsis and the eukaryotic microalgae to Chlorophyta. The unique fungal strain isolated was closely related to T. duponti. Through our study, isolated thermophilic bacteria, microalgae and fungi from the “Aguas Hediondas” geothermal spring were characterized and identified. This study represents one of the first extensive molecular characterizations of extremophile microbes in the Tropical Equatorial Andes.
Keywords. microbial diversity; DNA markers; extremophiles; phylogenetics
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Affiliation(s)
- Roque Rivas-Párraga
- Life science and Agriculture Department. Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador
| | - Andrés Izquierdo
- Life science and Agriculture Department. Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador Centro de Nanociencia y Nanotecnología (CENCINAT), Universidad de las Fuerzas Armadas ESPE, Av. Gral. Rumiñahui s/n, P.O. Box 171-5-231B, Sangolquí, Ecuador Ecuador Grupo de Investigación en Microbiología y Ambiente (GIMA), Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador
| | - Karen Sánchez
- School of Biological Sciences and Engineering, Yachay Tech University, San Miguel de Urcuqui, Ecuador
| | - Darío Bolaños-Guerrón
- Department of Earth Science and Constructions, Geographical and Environmental Engineering, Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador Centro de Nanociencia y Nanotecnología (CENCINAT), Universidad de las Fuerzas Armadas ESPE, Av. Gral. Rumiñahui s/n, P.O. Box 171-5-231B, Sangolquí, Ecuador Ecuador
| | - Alonzo Alfaro-Núñez
- Clinical Biochemistry Department, Næstved Hospital, Ringstegade 57a, 4700 Næstved, Denmark 5 Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353 Copenhagen K, Denmark
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26
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Madden AA, Oliverio AM, Kearns PJ, Henley JB, Fierer N, Starks PTB, Wolfe BE, Romero LM, Lattin CR. Chronic stress and captivity alter the cloacal microbiome of a wild songbird. J Exp Biol 2022; 225:274791. [DOI: 10.1242/jeb.243176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/07/2022] [Indexed: 11/20/2022]
Abstract
There are complex interactions between an organism's microbiome and its response to stressors, often referred to as the “gut-brain axis;” however, the ecological relevance of this axis in wild animals remains poorly understood. Here, we used a chronic mild stress protocol to induce stress in wild-caught house sparrows (Passer domesticus), and compared microbial communities among stressed animals, those recovering from stress, captive controls (unstressed), and a group not brought into captivity. We assessed changes in microbial communities and abundance of shed microbes by culturing cloacal samples on multiple media to select for aerobic and anaerobic bacteria and fungi. We complemented this with cultivation-independent 16S and ITS rRNA gene amplification and sequencing, pairing these results with host physiological and immune metrics, including body mass change, relative spleen mass, and plasma corticosterone concentrations. We found significant effects of stress and captivity on the house sparrow microbiomes, with stress leading to an increased relative abundance of endotoxin-producing bacteria— a possible mechanism for the hyperinflammatory response observed in captive avians. While we found evidence that the microbiome community partially recovers after stress cessation, animals may lose key taxa, and the abundance of endotoxin-producing bacteria persists. Our results suggest an overall link between chronic stress, host immune system, and the microbiome, with the loss of potentially beneficial taxa (e.g., lactic acid bacteria), and an increase in endotoxin-producing bacteria due to stress and captivity. Ultimately, consideration of the host's microbiome may be useful when evaluating the impact of stressors on individual and population health.
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Affiliation(s)
- Anne A. Madden
- Department of Biology, Tufts University, Medford, MA 02155, USA
- The Microbe Institute, Everett, MA, 02149, USA
| | - Angela M. Oliverio
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
- Yale School of the Environment, Yale University, 195 Prospect St., New Haven, CT, 06511, USA
| | | | - Jessica B. Henley
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | | | | | | | - Christine R. Lattin
- Department of Biology, Tufts University, Medford, MA 02155, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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Was the Last Bacterial Common Ancestor a Monoderm after All? Genes (Basel) 2022; 13:genes13020376. [PMID: 35205421 PMCID: PMC8871954 DOI: 10.3390/genes13020376] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 12/20/2022] Open
Abstract
The very nature of the last bacterial common ancestor (LBCA), in particular the characteristics of its cell wall, is a critical issue to understand the evolution of life on earth. Although knowledge of the relationships between bacterial phyla has made progress with the advent of phylogenomics, many questions remain, including on the appearance or disappearance of the outer membrane of diderm bacteria (also called Gram-negative bacteria). The phylogenetic transition between monoderm (Gram-positive bacteria) and diderm bacteria, and the associated peptidoglycan expansion or reduction, requires clarification. Herein, using a phylogenomic tree of cultivated and characterized bacteria as an evolutionary framework and a literature review of their cell-wall characteristics, we used Bayesian ancestral state reconstruction to infer the cell-wall architecture of the LBCA. With the same phylogenomic tree, we further revisited the evolution of the division and cell-wall synthesis (dcw) gene cluster using homology- and model-based methods. Finally, extensive similarity searches were carried out to determine the phylogenetic distribution of the genes involved with the biosynthesis of the outer membrane in diderm bacteria. Quite unexpectedly, our analyses suggest that all cultivated and characterized bacteria might have evolved from a common ancestor with a monoderm cell-wall architecture. If true, this would indicate that the appearance of the outer membrane was not a unique event and that selective forces have led to the repeated adoption of such an architecture. Due to the lack of phenotypic information, our methodology cannot be applied to all extant bacteria. Consequently, our conclusion might change once enough information is made available to allow the use of an even more diverse organism selection.
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Genome Sequence of Litorilinea aerophila, an Icelandic Intertidal Hot Springs Bacterium. Microbiol Resour Announc 2022; 11:e0120621. [PMID: 35084223 PMCID: PMC8793728 DOI: 10.1128/mra.01206-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The hot springs bacterium Litorilinea aerophila PRI-4131T (= ATCC BAA-2444T) was found in Isafjardardjup, in northwest Iceland. In this paper, we present a draft genome sequence for the type strain, with a total predicted genome length of 6,043,010 bp, 4,608 protein-coding sequences, 54 RNAs, 9 CRISPR arrays, and a G+C content of 64.61%.
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ElyC and Cyclic Enterobacterial Common Antigen Regulate Synthesis of Phosphoglyceride-Linked Enterobacterial Common Antigen. mBio 2021; 12:e0284621. [PMID: 34809459 PMCID: PMC8609368 DOI: 10.1128/mbio.02846-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Gram-negative cell envelope is a complex structure delineating the cell from its environment. Recently, we found that enterobacterial common antigen (ECA) plays a role maintaining the outer membrane (OM) permeability barrier, which excludes toxic molecules including many antibiotics. ECA is a conserved carbohydrate found throughout Enterobacterales (e.g., Salmonella, Klebsiella, and Yersinia). There are two OM forms of ECA (phosphoglyceride-linked ECAPG and lipopolysaccharide-linked ECALPS) and one periplasmic form of ECA (cyclic ECACYC). ECAPG, found in the outer leaflet of the OM, consists of a linear ECA oligomer attached to phosphoglyceride through a phosphodiester linkage. The process through which ECAPG is produced from polymerized ECA is unknown. Therefore, we set out to identify genes interacting genetically with ECAPG biosynthesis in Escherichia coli K-12 using the competition between ECA and peptidoglycan biosynthesis. Through transposon-directed insertion sequencing, we identified an interaction between elyC and ECAPG biosynthesis. ElyC is an inner membrane protein previously shown to alter peptidoglycan biosynthesis rates. We found ΔelyC was lethal specifically in strains producing ECAPG without other ECA forms, suggesting ECAPG biosynthesis impairment or dysregulation. Further characterization suggested ElyC inhibits ECAPG synthesis in a posttranscriptional manner. Moreover, the full impact of ElyC on ECA levels requires the presence of ECACYC. Our data demonstrate ECACYC can regulate ECAPG synthesis in strains wild type for elyC. Overall, our data demonstrate ElyC and ECACYC act in a novel pathway that regulates the production of ECAPG, supporting a model in which ElyC provides feedback regulation of ECAPG production based on the periplasmic levels of ECACYC.
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O’Donnell D, Sukovaty L, Webb G. Impact of Storage Conditions on Equine Fecal Inoculum for Estimating In Vitro Digestibility. Animals (Basel) 2021; 11:ani11113195. [PMID: 34827926 PMCID: PMC8614252 DOI: 10.3390/ani11113195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/05/2021] [Accepted: 11/07/2021] [Indexed: 11/22/2022] Open
Abstract
Simple Summary Sample handling and storage may affect the fermentative capacity of fecal inoculum. The need to collect rectal grabs from individuals can be a limiting factor in utilizing fecal inoculum from very young or feral animals. This study evaluated the effect of storage conditions of equine feces on the viability of microbial inoculum used for in vitro equine digestibility trials. Pooled fecal material was stored anaerobically at 39 °C for 15 min (control), while aerobic samples were stored at 22 °C for 6 h (SC1), 3 °C for 6 h (SC2), and −18 °C for 24 h (SC3). Results supported that fecal material stored aerobically for six hours at 22 °C provided similar digestibility estimates compared to the control, while dry matter digestibility decreased by 3.86% at SC2 and by 4.08% at SC3. Abstract This study evaluated the effect of storage conditions of equine fecal material on the viability of microbial inoculum used for in vitro equine digestibility trials. Pooled fecal material from three mature Quarter Horse geldings was stored at 39 °C anaerobically for 15 min (control), while aerobic samples were stored at 22 °C for 6 h (SC1), 3 °C for 6 h (SC2), and −18 °C for 24 h (SC3). Following storage, the feces were utilized to prepare microbial inoculum for the digestion of six different forages using the Daisy II Incubator. After incubation, DM, NDF, and ADF compositions were determined and used to calculate DMD, NDFD, and ADFD. Analysis using the OLS regression model for differences in DMD, NDFD, and ADFD across the storage conditions found significant interactions between the forage sample and the storage condition (p < 0.05). The results between the control and SC1, SC2, and SC3 were not different (p < 0.8). Fecal material stored aerobically for six hours at 22 °C provided similar digestibility estimates compared to the control, while DMD decreased by 3.86% in SC2 and by 4.08% in SC3.
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Rahman MU, Wang W, Sun Q, Shah JA, Li C, Sun Y, Li Y, Zhang B, Chen W, Wang S. Endolysin, a Promising Solution against Antimicrobial Resistance. Antibiotics (Basel) 2021; 10:1277. [PMID: 34827215 PMCID: PMC8614784 DOI: 10.3390/antibiotics10111277] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/14/2021] [Accepted: 10/16/2021] [Indexed: 12/24/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global crisis for human public health which threatens the effective prevention and control of ever-increasing infectious diseases. The advent of pandrug-resistant bacteria makes most, if not all, available antibiotics invalid. Meanwhile, the pipeline of novel antibiotics development stagnates, which prompts scientists and pharmacists to develop unconventional antimicrobials. Bacteriophage-derived endolysins are cell wall hydrolases which could hydrolyze the peptidoglycan layer from within and outside of bacterial pathogens. With high specificity, rapid action, high efficiency, and low risk of resistance development, endolysins are believed to be among the best alternative therapeutic agents to treat multidrug resistant (MDR) bacteria. As of now, endolysins have been applied to diverse aspects. In this review, we comprehensively introduce the structures and activities of endolysins and summarize the latest application progress of recombinant endolysins in the fields of medical treatment, pathogen diagnosis, food safety, and agriculture.
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Affiliation(s)
- Mujeeb ur Rahman
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
| | - Weixiao Wang
- Clinical Research Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing 210003, China;
| | - Qingqing Sun
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
| | - Junaid Ali Shah
- College of Life Sciences, Jilin University, Changchun 130012, China;
| | - Chao Li
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
| | - Yanmei Sun
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
| | - Yuanrui Li
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
| | - Bailing Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China;
| | - Wei Chen
- Clinical Research Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing 210003, China;
| | - Shiwei Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
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32
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Montgomery K, Williams TJ, Brettle M, Berengut JF, Zhang E, Zaugg J, Hugenholtz P, Ferrari BC. Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient-poor Antarctic soils. Environ Microbiol 2021; 23:4276-4294. [PMID: 34029441 DOI: 10.1111/1462-2920.15610] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 11/28/2022]
Abstract
Candidatus Dormibacterota is an uncultured bacterial phylum found predominantly in soil that is present in high abundances within cold desert soils. Here, we interrogate nine metagenome-assembled genomes (MAGs), including six new MAGs derived from soil metagenomes obtained from two eastern Antarctic sites. Phylogenomic and taxonomic analyses revealed these MAGs represent four genera and five species, representing two order-level clades within Ca. Dormibacterota. Metabolic reconstructions of these MAGs revealed the potential for aerobic metabolism, and versatile adaptations enabling persistence in the 'extreme' Antarctic environment. Primary amongst these adaptations were abilities to scavenge atmospheric H2 and CO as energy sources, as well as using the energy derived from H2 oxidation to fix atmospheric CO2 via the Calvin-Bassham-Benson cycle, using a RuBisCO type IE. We propose that these allow Ca. Dormibacterota to persist using H2 oxidation and grow using atmospheric chemosynthesis in terrestrial Antarctica. Fluorescence in situ hybridization revealed Ca. Dormibacterota to be coccoid cells, 0.3-1.4 μm in diameter, with some cells exhibiting the potential for a symbiotic or syntrophic lifestyle.
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Affiliation(s)
- Kate Montgomery
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Randwick, NSW, 2052, Australia
| | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Randwick, NSW, 2052, Australia
| | - Merryn Brettle
- Biomedical Imaging Facility, Mark Wainwright Analytical Centre, UNSW Sydney, Randwick, NSW, 2052, Australia
| | - Jonathan F Berengut
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Eden Zhang
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Randwick, NSW, 2052, Australia
| | - Julian Zaugg
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Qld, 4072, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Qld, 4072, Australia
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Randwick, NSW, 2052, Australia
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Salam N, Xian WD, Asem MD, Xiao M, Li WJ. From ecophysiology to cultivation methodology: filling the knowledge gap between uncultured and cultured microbes. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:132-147. [PMID: 37073336 PMCID: PMC10077289 DOI: 10.1007/s42995-020-00064-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/22/2020] [Indexed: 05/03/2023]
Abstract
Earth is dominated by a myriad of microbial communities, but the majority fails to grow under in situ laboratory conditions. The basic cause of unculturability is that bacteria dominantly occur as biofilms in natural environments. Earlier improvements in the culture techniques are mostly done by optimizing media components. However, with technological advancement particularly in the field of genome sequencing and cell imagining techniques, new tools have become available to understand the ecophysiology of microbial communities. Hence, it becomes easier to mimic environmental conditions in the culture plate. Other methods include co-culturing, emendation of growth factors, and cultivation after physical cell sorting. Most recently, techniques have been proposed for bacterial cultivation by employing genomic data to understand either microbial interactions (network-directed targeted bacterial isolation) or ecosystem engineering (reverse genomics). Hopefully, these techniques may be applied to almost all environmental samples, and help fill the gaps between the cultured and uncultured microbial communities.
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Affiliation(s)
- Nimaichand Salam
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Mipeshwaree Devi Asem
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Min Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011 China
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Roumia AF, Tsirigos KD, Theodoropoulou MC, Tamposis IA, Hamodrakas SJ, Bagos PG. OMPdb: A Global Hub of Beta-Barrel Outer Membrane Proteins. FRONTIERS IN BIOINFORMATICS 2021; 1:646581. [PMID: 36303794 PMCID: PMC9581022 DOI: 10.3389/fbinf.2021.646581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/18/2021] [Indexed: 11/14/2022] Open
Abstract
OMPdb (www.ompdb.org) was introduced as a database for β-barrel outer membrane proteins from Gram-negative bacteria in 2011 and then included 69,354 entries classified into 85 families. The database has been updated continuously using a collection of characteristic profile Hidden Markov Models able to discriminate between the different families of prokaryotic transmembrane β-barrels. The number of families has increased ultimately to a total of 129 families in the current, second major version of OMPdb. New additions have been made in parallel with efforts to update existing families and add novel families. Here, we present the upgrade of OMPdb, which from now on aims to become a global repository for all transmembrane β-barrel proteins, both eukaryotic and bacterial.
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Affiliation(s)
- Ahmed F. Roumia
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | | | | | - Ioannis A. Tamposis
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Stavros J. Hamodrakas
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Pantelis G. Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- *Correspondence: Pantelis G. Bagos
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35
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Ward LM, Fischer WW, McGlynn SE. Candidatus Anthektikosiphon siderophilum OHK22, a New Member of the Chloroflexi Family Herpetosiphonaceae from Oku-okuhachikurou Onsen. Microbes Environ 2021; 35. [PMID: 32727976 PMCID: PMC7511795 DOI: 10.1264/jsme2.me20030] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We report the draft metagenome-assembled genome of a member of the Chloroflexi family Herpetosiphonaceae from microbial biofilms developed in a circumneutral, iron-rich hot spring in Japan. This taxon represents a novel genus and species—here proposed as Candidatus Anthektikosiphon siderophilum—that expands the known taxonomic and genetic diversity of the Herpetosiphonaceae and helps orient the evolutionary history of key traits like photosynthesis and aerobic respiration in the Chloroflexi.
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Affiliation(s)
- Lewis M Ward
- Department of Earth & Planetary Sciences, Harvard University.,Earth-Life Science Institute, Tokyo Institute of Technology
| | - Woodward W Fischer
- Division of Geological & Planetary Sciences, California Institute of Technology
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36
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Gram-negative bacteria associated with a dominant arboreal ant species outcompete phyllosphere-associated bacteria species in a tropical canopy. Oecologia 2021; 195:959-970. [PMID: 33630170 DOI: 10.1007/s00442-021-04878-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/10/2021] [Indexed: 01/05/2023]
Abstract
Ants have efficient and well-studied social immunity mechanisms, which prevent the colony contamination. Little is known about how workers keep their outside territory clear of diseases. We investigated the interactions between Azteca chartifex ants, their associated bacteria and bacteria on the phyllosphere of Byrsonima sericea trees, comparing plants patrolled and not by the ants. The hypothesis is that bacteria associated with the worker's exoskeleton may outcompete the leaf bacteria. Culturable bacteria were isolated from ants, from the main and satellite nests, and from phyllosphere of B. sericea taken from trees that had A. chartifex nests and from trees without nests. The isolates were grouped by Gram guilds and identified at the genus level. There was a higher percentage of Gram-negative isolates in the ants and on the leaves patrolled by them. There was a higher growth rate of ant bacteria from the main nest compared to those found in ants from the satellite nests. The most representative genus among ant isolates was Enterobacter, also found on leaves patrolled by ants. Under favourable in vitro conditions, A. chartifex Gram-negative bacteria outcompete leaf bacteria by overgrowth, showing a greater competition capacity over the Gram-positive bacteria from leaves with no previous interaction with ants in the field. It was demonstrated that ants carry bacteria capable of outcompeting exogenous bacteria associated with their outside territory. The leaf microbiota of a patrolled tree could be shaped by the ant microbiota, suggesting that large ant colonies may have a key role in structuring canopy plant-microbe interactions.
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37
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Huang CY, Araujo K, Sánchez JN, Kund G, Trumble J, Roper C, Godfrey KE, Jin H. A stable antimicrobial peptide with dual functions of treating and preventing citrus Huanglongbing. Proc Natl Acad Sci U S A 2021; 118:e2019628118. [PMID: 33526689 PMCID: PMC8017978 DOI: 10.1073/pnas.2019628118] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Citrus Huanglongbing (HLB), caused by a vector-transmitted phloem-limited bacterium Candidatus Liberibacter asiaticus (CLas), is the most devastating citrus disease worldwide. Currently, there are no effective strategies to prevent infection or to cure HLB-positive trees. Here, using comparative analysis between HLB-sensitive citrus cultivars and HLB-tolerant citrus hybrids and relatives, we identified a novel class of stable antimicrobial peptides (SAMPs). The SAMP from Microcitrusaustraliasica can rapidly kill Liberibacter crescens (Lcr), a culturable Liberibacter strain, and inhibit infections of CLas and CL. solanacearum in plants. In controlled greenhouse trials, SAMP not only effectively reduced CLas titer and disease symptoms in HLB-positive trees but also induced innate immunity to prevent and inhibit infections. Importantly, unlike antibiotics, SAMP is heat stable, making it better suited for field applications. Spray-applied SAMP was taken up by citrus leaves, stayed stable inside the plants for at least a week, and moved systemically through the vascular system where CLas is located. We further demonstrate that SAMP is most effective on α-proteobacteria and causes rapid cytosol leakage and cell lysis. The α-helix-2 domain of SAMP is sufficient to kill Lcr Future field trials will help determine the efficacy of SAMP in controlling HLB and the ideal mode of application.
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Affiliation(s)
- Chien-Yu Huang
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Karla Araujo
- Contained Research Facility, University of California, Davis, CA 95616
| | - Jonatan Niño Sánchez
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Gregory Kund
- Department of Entomology, University of California, Riverside, CA 92521
| | - John Trumble
- Department of Entomology, University of California, Riverside, CA 92521
| | - Caroline Roper
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
| | | | - Hailing Jin
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521;
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38
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Xiong JQ, Cui P, Ru S, Govindwar SP, Kurade MB, Jang M, Kim SH, Jeon BH. Unravelling metabolism and microbial community of a phytobed co-planted with Typha angustifolia and Ipomoea aquatica for biodegradation of doxylamine from wastewater. JOURNAL OF HAZARDOUS MATERIALS 2021; 401:123404. [PMID: 32659588 DOI: 10.1016/j.jhazmat.2020.123404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
Pharmaceutical contaminants in environment induce unexpected effects on ecological systems and human; thus, development of efficient technologies for their removal is immensely necessary. In this study, biodegradation and metabolic fate of a frequently found pharmaceutical contaminant, doxylamine by Typha angustifolia and Ipomoea aquatica was investigated. Microbial community of the plant rhizosphere has been identified to understand the important roles of the functional microbes. The plants reduced 48-80.5 % of doxylamine through hydrolysis/dehydroxylation and carbonylation/decarbonylation. A constructed phytobed co-planted with T. angustifolia and I. aquatica removed 77.3 %, 100 %, 83.67 %, and 61.13 % of chemical oxygen demand, total nitrogen, total phosphorus, and doxylamine respectively from real wastewater. High-throughput sequencing of soil and rhizosphere indicated that the phyla Proteobacteria, Bacteroidetes, Firmicutes, Planctomycetes, Actinobacteria, and Cyanobacteria dominated the microbial communities of the phytobed. Current study has demonstrated the applicability of the developed phytobeds for the treatment of doxylamine from municipal wastewater and provide a comprehensive understanding of its metabolism through plant and its rhizospheric microbial communities.
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Affiliation(s)
- Jiu-Qiang Xiong
- College of Marine Life Science, Ocean University of China, Yushan 5, Qingdao, 266003, China
| | - Pengfei Cui
- College of Marine Life Science, Ocean University of China, Yushan 5, Qingdao, 266003, China
| | - Shaoguo Ru
- College of Marine Life Science, Ocean University of China, Yushan 5, Qingdao, 266003, China
| | - Sanjay P Govindwar
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Mayur B Kurade
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Min Jang
- Department of Environmental Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowun-gu, Seoul, 01897, South Korea
| | - Sang-Hyoun Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 03722, South Korea
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul, 04763, South Korea.
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39
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Megrian D, Taib N, Witwinowski J, Beloin C, Gribaldo S. One or two membranes? Diderm Firmicutes challenge the Gram-positive/Gram-negative divide. Mol Microbiol 2020; 113:659-671. [PMID: 31975449 DOI: 10.1111/mmi.14469] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 12/24/2022]
Abstract
How, when and why the transition between cell envelopes with one membrane (Gram-positives or monoderms) and two (Gram-negative or diderms) occurred in Bacteria is a key unanswered question in evolutionary biology. Different hypotheses have been put forward, suggesting that either the monoderm or the diderm phenotype is ancestral. The existence of diderm members in the classically monoderm Firmicutes challenges the Gram-positive/Gram-negative divide and provides a great opportunity to tackle the issue. In this review, we present current knowledge on the diversity of bacterial cell envelopes, including these atypical Firmicutes. We discuss how phylogenomic analysis supports the hypothesis that the diderm cell envelope architecture is an ancestral character in the Firmicutes, and that the monoderm phenotype in this phylum arose multiple times independently by loss of the outer membrane. Given the overwhelming distribution of diderm phenotypes with respect to monoderm ones, this scenario likely extends to the ancestor of all bacteria. Finally, we discuss the recent development of genetic tools for Veillonella parvula, a diderm Firmicute member of the human microbiome, which indicates it as an emerging new experimental model to investigate fundamental aspects of the diderm/monoderm transition.
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Affiliation(s)
- Daniela Megrian
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France.,Ecole Doctorale Complexité du vivant, Sorbonne University, Paris, France
| | - Najwa Taib
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France.,Hub Bioinformatics and Biostatistics, Department of Computational Biology, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Jerzy Witwinowski
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France
| | - Christophe Beloin
- Department of Microbiology, Genetics of Biofilm Unit, Institut Pasteur, Paris, France
| | - Simonetta Gribaldo
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France
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40
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Gautam J, Xu Z. Construction and Validation of a Genome-Scale Metabolic Network of Thermotoga sp. Strain RQ7. Appl Biochem Biotechnol 2020; 193:896-911. [PMID: 33200269 DOI: 10.1007/s12010-020-03470-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 11/09/2020] [Indexed: 11/30/2022]
Abstract
Thermotoga are anaerobic hyperthermophiles that have a deep lineage to the last universal ancestor and produce biological hydrogen gas accompanying cell growth. In recent years, systems-level approaches have been used to elucidate their metabolic capacities, by integrating mathematical modeling and experimental results. To assist biochemical engineering studies of T. sp. strain RQ7, this work aims at building a metabolic model of the bacterium that quantitatively simulates its metabolism at the genome scale. The constructed model, RQ7_iJG408, consists of 408 genes, 692 reactions, and 538 metabolites. Constraint-based flux balance analyses were used to simulate cell growth in both the complex and defined media. Quantitative comparison of the predicted and measured growth rates resulted in good agreements. This model serves as a foundation for an integrated biochemical description of T. sp. strain RQ7. It is a useful tool in designing growth media, identifying metabolic engineering strategies, and exploiting the physiological potentials of this biotechnologically significant organism.
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Affiliation(s)
- Jyotshana Gautam
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Zhaohui Xu
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.
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41
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de Jonge PA, Smit Sibinga DJC, Boright OA, Costa AR, Nobrega FL, Brouns SJJ, Dutilh BE. Development of Styrene Maleic Acid Lipid Particles as a Tool for Studies of Phage-Host Interactions. J Virol 2020; 94:e01559-20. [PMID: 32938760 PMCID: PMC7654272 DOI: 10.1128/jvi.01559-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 01/08/2023] Open
Abstract
The infection of a bacterium by a phage starts with attachment to a receptor molecule on the host cell surface by the phage. Since receptor-phage interactions are crucial to successful infections, they are major determinants of phage host range and, by extension, of the broader effects that phages have on bacterial communities. Many receptor molecules, particularly membrane proteins, are difficult to isolate because their stability is supported by their native membrane environments. Styrene maleic acid lipid particles (SMALPs), a recent advance in membrane protein studies, are the result of membrane solubilizations by styrene maleic acid (SMA) copolymer chains. SMALPs thereby allow for isolation of membrane proteins while maintaining their native environment. Here, we explore SMALPs as a tool to isolate and study phage-receptor interactions. We show that SMALPs produced from taxonomically distant bacterial membranes allow for receptor-specific decrease of viable phage counts of several model phages that span the three largest phage families. After characterizing the effects of incubation time and SMALP concentration on the activity of three distinct phages, we present evidence that the interaction between two model phages and SMALPs is specific to bacterial species and the phage receptor molecule. These interactions additionally lead to DNA ejection by nearly all particles at high phage titers. We conclude that SMALPs are a potentially highly useful tool for phage-host interaction studies.IMPORTANCE Bacteriophages (viruses that infect bacteria or phages) impact every microbial community. All phage infections start with the binding of the viral particle to a specific receptor molecule on the host cell surface. Due to its importance in phage infections, this first step is of interest to many phage-related research and applications. However, many phage receptors are difficult to isolate. Styrene maleic acid lipid particles (SMALPs) are a recently developed approach to isolate membrane proteins in their native environment. In this study, we explore SMALPs as a tool to study phage-receptor interactions. We find that different phage species bind to SMALPs, while maintaining specificity to their receptor. We then characterize the time and concentration dependence of phage-SMALP interactions and furthermore show that they lead to genome ejection by the phage. The results presented here show that SMALPs are a useful tool for future studies of phage-receptor interactions.
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Affiliation(s)
- Patrick A de Jonge
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Dieuwke J C Smit Sibinga
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Oliver A Boright
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Ana Rita Costa
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
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42
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Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition. Nat Ecol Evol 2020; 4:1661-1672. [PMID: 33077930 DOI: 10.1038/s41559-020-01299-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 08/05/2020] [Indexed: 11/08/2022]
Abstract
The transition between cell envelopes with one membrane (Gram-positive or monoderm) and those with two membranes (Gram-negative or diderm) is a fundamental open question in the evolution of Bacteria. Evidence of the presence of two independent diderm lineages, the Halanaerobiales and the Negativicutes, within the classically monoderm Firmicutes has blurred the monoderm/diderm divide and specifically anticipated that other members with an outer membrane (OM) might exist in this phylum. Here, by screening 1,639 genomes of uncultured Firmicutes for signatures of an OM, we highlight a third and deep branching diderm clade, the Limnochordia, strengthening the hypothesis of a diderm ancestor and the occurrence of independent transitions leading to the monoderm phenotype. Phyletic patterns of over 176,000 protein families constituting the Firmicutes pan-proteome identify those that strongly correlate with the diderm phenotype and suggest the existence of new potential players in OM biogenesis. In contrast, we find practically no largely conserved core of monoderms, a fact possibly linked to different ways of adapting to repeated OM losses. Phylogenetic analysis of a concatenation of main OM components totalling nearly 2,000 amino acid positions illustrates the common origin and vertical evolution of most diderm bacterial envelopes. Finally, mapping the presence/absence of OM markers onto the tree of Bacteria shows the overwhelming presence of diderm phyla and the non-monophyly of monoderm ones, pointing to an early origin of two-membraned cells and the derived nature of the Gram-positive envelope following multiple OM losses.
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43
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Gaisin VA, Kooger R, Grouzdev DS, Gorlenko VM, Pilhofer M. Cryo-Electron Tomography Reveals the Complex Ultrastructural Organization of Multicellular Filamentous Chloroflexota ( Chloroflexi) Bacteria. Front Microbiol 2020; 11:1373. [PMID: 32670237 PMCID: PMC7332563 DOI: 10.3389/fmicb.2020.01373] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/27/2020] [Indexed: 11/13/2022] Open
Abstract
The cell biology of Chloroflexota is poorly studied. We applied cryo-focused ion beam milling and cryo-electron tomography to study the ultrastructural organization of thermophilic Roseiflexus castenholzii and Chloroflexus aggregans, and mesophilic “Ca. Viridilinea mediisalina.” These species represent the three main lineages within a group of multicellular filamentous anoxygenic phototrophic Chloroflexota bacteria belonging to the Chloroflexales order. We found surprising structural complexity in the Chloroflexales. As with filamentous cyanobacteria, cells of C. aggregans and “Ca. Viridilinea mediisalina” share the outer membrane-like layers of their intricate multilayer cell envelope. Additionally, cells of R. castenholzii and “Ca. Viridilinea mediisalina” are connected by septal channels that resemble cyanobacterial septal junctions. All three strains possess long pili anchored close to cell-to-cell junctions, a morphological feature comparable to that observed in cyanobacteria. The cytoplasm of the Chloroflexales bacteria is crowded with intracellular organelles such as different types of storage granules, membrane vesicles, chlorosomes, gas vesicles, chemoreceptor-like arrays, and cytoplasmic filaments. We observed a higher level of complexity in the mesophilic strain compared to the thermophilic strains with regards to the composition of intracellular bodies and the organization of the cell envelope. The ultrastructural details that we describe in these Chloroflexales bacteria will motivate further cell biological studies, given that the function and evolution of the many discovered morphological traits remain enigmatic in this diverse and widespread bacterial group.
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Affiliation(s)
- Vasil A Gaisin
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.,Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Romain Kooger
- Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Denis S Grouzdev
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Vladimir M Gorlenko
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Martin Pilhofer
- Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020. [PMID: 31900730 DOI: 10.1007/s00709-019-01442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020; 257:621-753. [PMID: 31900730 PMCID: PMC7203096 DOI: 10.1007/s00709-019-01442-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/19/2019] [Indexed: 05/02/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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Farci D, Aksoyoglu MA, Farci SF, Bafna JA, Bodrenko I, Ceccarelli M, Kirkpatrick J, Winterhalter M, Kereïche S, Piano D. Structural insights into the main S-layer unit of Deinococcus radiodurans reveal a massive protein complex with porin-like features. J Biol Chem 2020; 295:4224-4236. [PMID: 32071085 PMCID: PMC7105295 DOI: 10.1074/jbc.ra119.012174] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 02/13/2020] [Indexed: 11/06/2022] Open
Abstract
In the extremophile bacterium Deinococcus radiodurans, the outermost surface layer is tightly connected with the rest of the cell wall. This integrated organization provides a compact structure that shields the bacterium against environmental stresses. The fundamental unit of this surface layer (S-layer) is the S-layer deinoxanthin-binding complex (SDBC), which binds the carotenoid deinoxanthin and provides both, thermostability and UV radiation resistance. However, the structural organization of the SDBC awaits elucidation. Here, we report the isolation of the SDBC with a gentle procedure consisting of lysozyme treatment and solubilization with the nonionic detergent n-dodecyl-β-d-maltoside, which preserved both hydrophilic and hydrophobic components of the SDBC and allows the retention of several minor subunits. As observed by low-resolution single-particle analysis, we show that the complex possesses a porin-like structural organization, but is larger than other known porins. We also noted that the main SDBC component, the protein DR_2577, shares regions of similarity with known porins. Moreover, results from electrophysiological assays with membrane-reconstituted SDBC disclosed that it is a nonselective channel that has some peculiar gating properties, but also exhibits behavior typically observed in pore-forming proteins, such as porins and ionic transporters. The functional properties of this system and its porin-like organization provide information critical for understanding ion permeability through the outer cell surface of S-layer-carrying bacterial species.
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Affiliation(s)
- Domenica Farci
- Department of Plant Physiology, Warsaw University of Life Sciences-SGGW, Nowoursynowska Str. 159, 02776 Warsaw, Poland.
| | | | - Stefano Francesco Farci
- Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, University of Cagliari, V.le S. Ignazio da Laconi 13, 09123 Cagliari, Italy
| | - Jayesh Arun Bafna
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759 Bremen, Germany
| | - Igor Bodrenko
- Department of Physics and IOM/CNR, University of Cagliari, 09042 Monserrato, Italy
| | - Matteo Ceccarelli
- Department of Physics and IOM/CNR, University of Cagliari, 09042 Monserrato, Italy
| | - Joanna Kirkpatrick
- Leibniz Institute on Ageing-Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany; The Francis Crick Institute, 1 Midland Road, NW1 1AT London, United Kingdom
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759 Bremen, Germany
| | - Sami Kereïche
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague 128 00, Czech Republic.
| | - Dario Piano
- Department of Plant Physiology, Warsaw University of Life Sciences-SGGW, Nowoursynowska Str. 159, 02776 Warsaw, Poland.
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Kochetkova TV, Zayulina KS, Zhigarkov VS, Minaev NV, Chichkov BN, Novikov AA, Toshchakov SV, Elcheninov AG, Kublanov IV. Tepidiforma bonchosmolovskayae gen. nov., sp. nov., a moderately thermophilic Chloroflexi bacterium from a Chukotka hot spring (Arctic, Russia), representing a novel class, Tepidiformia, which includes the previously uncultivated lineage OLB14. Int J Syst Evol Microbiol 2020; 70:1192-1202. [PMID: 31769750 DOI: 10.1099/ijsem.0.003902] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel aerobic moderately thermophilic bacterium, strain 3753OT, was isolated from a Chukotka hot spring (Arctic, Russia) using the newly developed technology of laser engineering of microbial systems. Сells were regular short rods, 0.4×0.8-2.0 µm in size, with a monoderm-type envelope and a single flagellum. The temperature and pH ranges for growth were 42-60 °C and pH 6.5-8.5, the optima being 50-54 °C and pH 7.3. Strain 3753OT grew chemoorganoheterotrophically on a number of carbohydrates or peptidic substrates and volatile fatty acids, and chemolithoautotrophically with siderite (FeCO3) as the electron donor. The major cellular fatty acid was branched C19 : 0. Phosphatidylethanolamine, phosphatidylglycerol and two unidentified phospholipids as well as two yellow carotenoid-type pigments were detected in the polar lipid extract. Strain 3753OT was inhibited by chloramphenicol, polymyxin B, vancomycin, streptomycin, neomycin and kanamycin, but resistant to the action of novobiocin and ampicillin. The DNA G+C content was 69.9 mol%. The 16S rRNA gene as well as 51 conservative protein sequence-based phylogenetic analyses placed strain 3753OT within the previously uncultivated lineage OLB14 in the phylum Chloroflexi. Taking into account the phylogenetic position as well as phenotypic properties of the novel isolate, the novel genus and species Tepidiforma bonchosmolovskayae gen. nov., sp. nov., within the Tepidiformaceae fam. nov., the Tepidiformales ord. nov. and the Tepidiformia classis nov. are proposed. The type strain of Tepidiforma bonchosmolovskayae is 3753OT (=VKM B-3389T=KTCT 72284T).
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Affiliation(s)
- Tatiana V Kochetkova
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 60-let Oktyabrya prospect 7/2, Russia
| | - Kseniya S Zayulina
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 60-let Oktyabrya prospect 7/2, Russia
| | - Vyacheslav S Zhigarkov
- Institute of Photon Technologies of Federal Scientific Research Centre "Crystallography and Photonics" of the Russian Academy of Sciences, Moscow, Troitsk, Pionerskaya, Russia
| | - Nikita V Minaev
- Institute of Photon Technologies of Federal Scientific Research Centre "Crystallography and Photonics" of the Russian Academy of Sciences, Moscow, Troitsk, Pionerskaya, Russia
| | - Boris N Chichkov
- Institute of Photon Technologies of Federal Scientific Research Centre "Crystallography and Photonics" of the Russian Academy of Sciences, Moscow, Troitsk, Pionerskaya, Russia
| | | | - Stepan V Toshchakov
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 60-let Oktyabrya prospect 7/2, Russia
| | - Alexander G Elcheninov
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 60-let Oktyabrya prospect 7/2, Russia
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 60-let Oktyabrya prospect 7/2, Russia
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Thermotogales origin scenario of eukaryogenesis. J Theor Biol 2020; 492:110192. [PMID: 32044287 DOI: 10.1016/j.jtbi.2020.110192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 02/06/2020] [Indexed: 12/11/2022]
Abstract
How eukaryotes were generated is an enigma of evolutionary biology. Widely accepted archaeal-origin eukaryogenesis scenarios, based on similarities of genes and related characteristics between archaea and eukaryotes, cannot explain several eukaryote-specific features of the last eukaryotic common ancestor, such as glycerol-3-phosphate-type membrane lipids, large cells and genomes, and endomembrane formation. Thermotogales spheroids, having multicopy-integrated large nucleoids and producing progeny in periplasm, may explain all of these features as well as endoplasmic reticulum-type signal cleavage sites, although they cannot divide. We hypothesize that the progeny chromosome is formed by random joining small DNAs in immature progeny, followed by reorganization by mechanisms including homologous recombination enabled with multicopy-integrated large genome (MILG). We propose that Thermotogales ancestor spheroids came to divide owing to the archaeal cell division genes horizontally transferred via virus-related particles, forming the first eukaryotic common ancestor (FECA). Referring to the hypothesis, the archaeal information-processing system would have been established in FECA by random joining DNAs excised from the MILG, which contained horizontally transferred archaeal and bacterial DNAs, followed by reorganization by the MILG-enabled homologous recombination. Thus, the large genome may have been a prerequisite, but not a consequence, of eukaryogenesis. The random joining of DNAs likely provided the basic mechanisms for eukaryotic evolution: producing the diversity by the formations of supergroups, novel genes, and introns that are involved in exon shuffling.
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Yan H, Ma D, Yang S, Ni Z, Fang W. Effluent lipopolysaccharide is a prompt marker of peritoneal dialysis-related gram-negative peritonitis. Perit Dial Int 2020; 40:455-461. [PMID: 32063187 DOI: 10.1177/0896860819896134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND To investigate the value of effluent lipopolysaccharide (LPS) for early detection of gram-negative peritonitis (GNP) in peritoneal dialysis (PD) patients. METHODS PD-related peritonitis episodes occurring between January 2016 and December 2018 were included in the study. Effluent LPS and the other infectious parameters were measured at peritonitis presentation, and peritonitis was categorized as GNP, non-GNP, and culture-negative peritonitis. Receiver operating characteristic (ROC) analysis was employed to evaluate the efficacy of effluent LPS to distinguish GNP. RESULTS A total of 161 peritonitis episodes were analyzed, including 49 GNP episodes and 82 non-GNP episodes. In contrast with non-GNP, GNP presented with higher effluent leukocyte count (3236 (1497-6144) vs. 1904 (679-4071) cell mm-3, p = 0.008), increased effluent LPS (1.552 (0.502-2.500) vs. 0.016 (0.010-0.030) EU mL-1, p < 0.001), lower blood leukocyte count (9.95 ± 3.18 vs. 11.56 ± 4.37 × 109 L-1, p = 0.017), greater neutrophil predominance (87.1 ± 4.6% vs. 83.4 ± 7.7%, p = 0.001), and greater "procalcitonin" (PCT, 4.90 (2.20-12.60) vs. 1.00 (0.51-4.07) µg L-1, p < 0.001). It took 5.2 ± 3.1 h to report the results of effluent LPS. Effluent LPS cutoff value of >0.035 EU mL-1 showed an area under the ROC curve of 0.972 (95% CI 0.951-0.994, p < 0.001) in differentiating GNP from non-GNP with a sensitivity of 100% and a specificity of 80.5%, and its joint utilization with PCT further increased the specificity (91.4%) to discriminate GNP. CONCLUSIONS PD effluent LPS could be an applicable early marker of gram-negative organism-related peritonitis in PD patients.
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Affiliation(s)
- Hao Yan
- Department of Nephrology, Renji Hospital, School of Medicine, 71140Shanghai Jiaotong University, People's Republic of China.,Shanghai Center for Peritoneal Dialysis Research, People's Republic of China
| | - Dahua Ma
- Department of Nephrology, Renji Hospital, School of Medicine, 71140Shanghai Jiaotong University, People's Republic of China.,Shanghai Center for Peritoneal Dialysis Research, People's Republic of China
| | - Shuang Yang
- Department of Clinical Laboratory, Renji Hospital, School of Medicine, 71140Shanghai Jiaotong University, People's Republic of China
| | - Zhaohui Ni
- Department of Nephrology, Renji Hospital, School of Medicine, 71140Shanghai Jiaotong University, People's Republic of China.,Shanghai Center for Peritoneal Dialysis Research, People's Republic of China
| | - Wei Fang
- Department of Nephrology, Renji Hospital, School of Medicine, 71140Shanghai Jiaotong University, People's Republic of China.,Shanghai Center for Peritoneal Dialysis Research, People's Republic of China
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50
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The Gut Microbiome and Type 2 Diabetes Mellitus: Discussing a Complex Relationship. Biomedicines 2020; 8:biomedicines8010008. [PMID: 31936158 PMCID: PMC7168169 DOI: 10.3390/biomedicines8010008] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/02/2020] [Accepted: 01/05/2020] [Indexed: 02/06/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) is a disease that affects over 9% of the United States population and is closely linked to obesity. While obesity was once thought to stem from a sedentary lifestyle and diets high in fat, recent evidence supports the idea that there is more complexity pertinent to the issue. The human gut microbiome has recently been the focus in terms of influencing disease onset. Evidence has shown that the microbiome may be more closely related to T2DM than what was originally thought. High fat diets typically result in poor microbiome heath, which then shifts the gut into a state of dysbiosis. Dysbiosis can then lead to metabolic deregulation, including increased insulin resistance and inflammation, two key factors in the development of T2DM. The purpose of this review is to discuss how microbiome relates to T2DM onset, especially considering obesity, insulin resistance, and inflammation.
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