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Crosby-Durrani HE, Carter SD, Blowey RW, Evans NJ. Molecular Screening for Digital Dermatitis-Associated Treponemes in Bovine Ischaemic Teat Necrosis Lesions and Milk in Dairy Cattle. Pathogens 2024; 13:427. [PMID: 38787279 PMCID: PMC11123857 DOI: 10.3390/pathogens13050427] [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: 03/18/2024] [Revised: 04/30/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024] Open
Abstract
Bovine ischaemic teat necrosis (ITN) is a disease affecting the skin of the teats of dairy cows with an unknown aetiopathogenesis. Digital dermatitis (DD)-associated treponemes have previously been suggested as a potential aetiological agent in ITN, although the sample size was small. The current study, using established PCR techniques, aimed to examine the association with the presence of DD-associated treponemes in a large number of ITN samples from a wider geographical area, and surveyed the potential of milk as an infection reservoir. From 95 ITN lesions, 35.8% (n = 34) were positive for at least one DD-associated treponeme compared with only 5.6% (n = 1) of 18 non-lesioned teats from cows with ITN lesions on a different teat using a nested PCR approach. All 10 age- and production-matched control cows were negative for DD-associated treponemes via PCR. No DD-associated treponemes could be detected from foremilk of cows with (n = 19) and without (n = 31) a DD lesion on the hind feet. DD-associated treponemes could be detected via PCR after incubation in milk for up to 2 h. Therefore, milk does not appear to be a competent reservoir for transmission of DD-associated treponemes. Moreover, in the current study DD-associated treponemes were only detected in a subset of ITN samples, so it is unlikely these opportunistic skin-associated pathogens are the major or sole agent of ITN.
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Affiliation(s)
- Hayley E. Crosby-Durrani
- Institute of Infection, Veterinary, and Ecological Sciences, University of Liverpool, Leahurst Campus, Chester High Road, Neston CH64 7TE, UK
| | - Stuart D. Carter
- Institute of Infection, Veterinary, and Ecological Sciences, University of Liverpool, Leahurst Campus, Chester High Road, Neston CH64 7TE, UK
| | | | - Nicholas J. Evans
- Institute of Infection, Veterinary, and Ecological Sciences, University of Liverpool, Leahurst Campus, Chester High Road, Neston CH64 7TE, UK
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2
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Hackmann TJ, Zhang B. The phenotype and genotype of fermentative prokaryotes. SCIENCE ADVANCES 2023; 9:eadg8687. [PMID: 37756392 PMCID: PMC10530074 DOI: 10.1126/sciadv.adg8687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023]
Abstract
Fermentation is a type of metabolism pervasive in oxygen-deprived environments. Despite its importance, we know little about the range and traits of organisms that carry out this metabolism. Our study addresses this gap with a comprehensive analysis of the phenotype and genotype of fermentative prokaryotes. We assembled a dataset with phenotypic records of 8350 organisms plus 4355 genomes and 13.6 million genes. Our analysis reveals fermentation is both widespread (in ~30% of prokaryotes) and complex (forming ~300 combinations of metabolites). Furthermore, it points to previously uncharacterized proteins involved in this metabolism. Previous studies suggest that metabolic pathways for fermentation are well understood, but metabolic models built in our study show gaps in our knowledge. This study demonstrates the complexity of fermentation while showing that there is still much to learn about this metabolism. All resources in our study can be explored by the scientific community with an online, interactive tool.
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Affiliation(s)
| | - Bo Zhang
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA
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3
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Yuan C, Xu W, Zhao C, Gao W, Wu G. Case Report: Detection of Treponema phagedenis in cerebrospinal fluid of a neurosyphilis patient by metagenomic next-generation sequencing. Front Cell Infect Microbiol 2023; 13:1218049. [PMID: 37712061 PMCID: PMC10497860 DOI: 10.3389/fcimb.2023.1218049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023] Open
Abstract
Treponema phagedenis, a human commensal spirochete, has been reported world-wide as a key factor in the pathogenesis of bovine digital dermatitis. Here we report a case of T. phagedenis sequence detection in the cerebrospinal fluid (CSF) of a patient. The patient was diagnosed with neurosyphilis, and T. phagedenis was detected as the only microorganism in his CSF by metagenomic sequencing. The patient went through a round of penicillin therapy previously (2.4 million units of Benzathine Penicillin intramuscularly once a week for three weeks) that did not resolve the symptoms; after the diagnosis of neurosyphilis he was treated with Penicillin G Sodium 4.0 million units q4h intravenous for 14 days then his symptoms resolved. To the best of our knowledge, T. phagedenis has never been reported to be detected in a human's CSF before. This was also the first time it was detected by metagenomic next-generation sequencing. We propose that more etiological tests should be performed including culture and sequencing for more patients with syphilis, which will contribute to a deeper understanding of the pathogenicity of the spirochete.
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Affiliation(s)
- Chenyan Yuan
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu, China
- Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, Jiangsu, China
| | - Wei Xu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu, China
- Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, Jiangsu, China
| | - Chenggui Zhao
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu, China
- Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, Jiangsu, China
| | - Wei Gao
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu, China
- Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, Jiangsu, China
| | - Guoqiu Wu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu, China
- Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, Jiangsu, China
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing, Jiangsu, China
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Belkhou C, Tadeo RT, Bacigalupe R, Valles-Colomer M, Chaffron S, Joossens M, Obregon A, Marín Reyes L, Trujillo O, Huys GRB, Raes J. Treponema peruense sp. nov., a commensal spirochaete isolated from human faeces. Int J Syst Evol Microbiol 2021; 71. [PMID: 34672919 PMCID: PMC8604162 DOI: 10.1099/ijsem.0.005050] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A Gram-stain-negative, obligatory anaerobic spirochaete (RCC2812T) was isolated from a faecal sample obtained from an individual residing in a remote Amazonian community in Peru. The bacterium showed highest 16S rRNA gene sequence similarity to the pig intestinal spirochete Treponema succinifaciens (89.48 %). Average nucleotide identity values between strain RCC2812T and all available Treponema genomes from validated type strains were all <73 %, thus clearly lower than the species delineation threshold. The DNA G+C content of RCC2812T was 41.24 mol%. Phenotypic characterization using the API-ZYM and API 20A systems confirmed the divergent position of this bacterium within the genus Treponema. Strain RCC2812T could be differentiated from the phylogenetically most closely related T. succinifaciens by the presence of alkaline phosphatase and α -glucosidase activities. Unlike T. succinifaciens, strain RCC2812T grew equally well with or without serum. Strain RCC2812T is the first commensal Treponema isolated from the human faecal microbiota of remote populations, and based on the collected data represents a novel Treponema species for which the name Treponema peruense sp. nov. is proposed. The type strain is RCC2812T (=LMG 31794T=CIP 111910T).
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Affiliation(s)
- Claire Belkhou
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Leuven, Belgium
| | - Raul Tito Tadeo
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Leuven, Belgium
| | - Rodrigo Bacigalupe
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Leuven, Belgium
| | - Mireia Valles-Colomer
- Centre for Integrative Biology (CIBIO), Università degli Studi di Trento (UNITN), Trento, Italy
| | | | - Marie Joossens
- Department of Biochemistry and microbiology, Universiteit Gent, Gent, Belgium
| | - Alexandra Obregon
- Department of Genetic Counseling, College of Health Professions, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Luis Marín Reyes
- Centro Nacional de Salud Publica, Instituto Nacional de Salud, Lima, Peru
| | - Omar Trujillo
- Centro Nacional de Salud Intercultural, Instituto Nacional de Salud, Lima, Peru
| | - Geert R B Huys
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Leuven, Belgium
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Leuven, Belgium
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5
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Trevisan G, Cinco M, Trevisini S, di Meo N, Chersi K, Ruscio M, Forgione P, Bonin S. Borreliae Part 1: Borrelia Lyme Group and Echidna-Reptile Group. BIOLOGY 2021; 10:biology10101036. [PMID: 34681134 PMCID: PMC8533607 DOI: 10.3390/biology10101036] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/06/2021] [Accepted: 10/09/2021] [Indexed: 12/17/2022]
Abstract
Simple Summary Borreliae are spirochaetes, which represent a heterogeneous phylum within bacteria. Spirochaetes are indeed distinguished from other bacteria for their spiral shape, which also characterizes Borreliae. This review describes briefly the organization of the phylum Spirocheteales with a digression about its pathogenicity and historical information about bacteria isolation and characterization. Among spirochaetes, Borrelia genus is here divided into three groups, namely the Lyme group (LG), the Echidna-Reptile group (REPG) and the Relapsing Fever group (RFG). Borreliae Part 1 deals with Lyme group and Echidna-Reptile group Borreliae, while the subject of Borreliae Part 2 is Relapsing Fever group and unclassified Borreliae. Lyme group Borreliae is organized here in sections describing ecology, namely tick vectors and animal hosts, epidemiology, microbiology, and Borrelia genome organization and antigen characterization. Furthermore, the main clinical manifestations in Lyme borreliosis are also described. Although included in the Lyme group due to their particular clinical features, Borrelia causing Baggio Yoshinari syndrome and Borrelia mayonii are described in dedicated paragraphs. The Borrelia Echidna-Reptile group has been recently characterized including spirochaetes that apparently are not pathogenic to humans, but infect reptiles and amphibians. The paragraph dedicated to this group of Borreliae describes their vectors, hosts, geographical distribution and their characteristics. Abstract Borreliae are divided into three groups, namely the Lyme group (LG), the Echidna-Reptile group (REPG) and the Relapsing Fever group (RFG). Currently, only Borrelia of the Lyme and RF groups (not all) cause infection in humans. Borreliae of the Echidna-Reptile group represent a new monophyletic group of spirochaetes, which infect amphibians and reptiles. In addition to a general description of the phylum Spirochaetales, including a brief historical digression on spirochaetosis, in the present review Borreliae of Lyme and Echidna-Reptile groups are described, discussing the ecology with vectors and hosts as well as microbiological features and molecular characterization. Furthermore, differences between LG and RFG are discussed with respect to the clinical manifestations. In humans, LG Borreliae are organotropic and cause erythema migrans in the early phase of the disease, while RFG Borreliae give high spirochaetemia with fever, without the development of erythema migrans. With respect of LG Borreliae, recently Borrelia mayonii, with intermediate characteristics between LG and RFG, has been identified. As part of the LG, it gives erythema migrans but also high spirochaetemia with fever. Hard ticks are vectors for both LG and REPG groups, but in LG they are mostly Ixodes sp. ticks, while in REPG vectors do not belong to that genus.
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Affiliation(s)
- Giusto Trevisan
- DSM—Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (G.T.); (N.d.M.)
| | - Marina Cinco
- DSV—Department of Life Sciences, University of Trieste, 34127 Trieste, Italy;
| | - Sara Trevisini
- ASUGI—Azienda Sanitaria Universitaria Giuliano Isontina, 34129 Trieste, Italy; (S.T.); (K.C.); (M.R.)
| | - Nicola di Meo
- DSM—Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (G.T.); (N.d.M.)
- ASUGI—Azienda Sanitaria Universitaria Giuliano Isontina, 34129 Trieste, Italy; (S.T.); (K.C.); (M.R.)
| | - Karin Chersi
- ASUGI—Azienda Sanitaria Universitaria Giuliano Isontina, 34129 Trieste, Italy; (S.T.); (K.C.); (M.R.)
| | - Maurizio Ruscio
- ASUGI—Azienda Sanitaria Universitaria Giuliano Isontina, 34129 Trieste, Italy; (S.T.); (K.C.); (M.R.)
| | - Patrizia Forgione
- UOSD Dermatologia, Centro Rif. Regionale Malattia di Hansen e Lyme, P.O. dei Pellegrini, ASL Napoli 1 Centro, 80145 Naples, Italy;
| | - Serena Bonin
- DSM—Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (G.T.); (N.d.M.)
- Correspondence: ; Tel.: +39-040-3993266
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Gleason CB, Settlage RE, Beckett LM, White RR. Characterizing Effects of Ingredients Differing in Ruminally Degradable Protein and Fiber Supplies on the Ovine Rumen Microbiome Using Next-Generation Sequencing. FRONTIERS IN ANIMAL SCIENCE 2021. [DOI: 10.3389/fanim.2021.745848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The ratio of concentrate to forage within diets is known to alter rumen microbial profiles, but comparatively less information is available on the effect of differing sources of individual nutrients on the microbiome. The objective of this study was to investigate rumen microbial responses to diets composed of protein and fiber sources expected to vary in nutrient degradability. The responses of interest included relative abundances of bacterial taxa as well as estimations of community richness and diversity. Ten ruminally cannulated wethers (Suffolk, Dorset, or Suffolk × Dorset) received four diet treatments consisting of either beet pulp or timothy hay and soybean meal (SBM) or heat-treated soybean meal (HSBM) in a partially replicated 4 × 4 Latin square experiment for 21 days. Timothy hay and beet pulp were expected to provide differing rumen degradabilities of neutral detergent fiber (NDF) while the soybean meals were expected to provide differing rumen degradabilities of crude protein (CP). Solid and liquid samples of rumen contents were collected for microbial DNA isolation and Next-Generation sequencing. Numerous rumen bacterial population shifts were observed due to change in fiber source, with increased abundances (P < 0.05) of fibrolytic populations associated with timothy hay diets compared with beet pulp diets. Conversely, populations of the pectin-degrading genera, Treponema and Lachnospira, increased on the beet pulp treatment (P = 0.015 and P = 0.0049, respectively). Limited impact on bacterial taxa was observed between diets differing in protein source. The Paraprevotellaceae genus YRC22 was observed to increase in abundance on HSBM diets (P = 0.023) and the phylum Spirochaetes tended to be more abundant on SBM than HSBM diets (P = 0.071). Beet pulp decreased rumen bacterial diversity (P = 0.0027) and tended to decrease bacterial species richness (P = 0.051) compared to timothy hay. Our results serve to further underscore the sensitivity of rumen microbes to changes in their preferred substrates, particularly of those associated with fiber degradation.
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Belkacemi S, Tidjani Alou M, Khelaifia S, Raoult D. A review of in vitro attempts to develop the axenic culture of Treponema pallidum and genomics-based suggestions to achieve this elusive goal. J Med Microbiol 2021; 70. [PMID: 34328411 DOI: 10.1099/jmm.0.001388] [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: 11/18/2022] Open
Abstract
To date, the axenic culture of Treponema pallidum remains a challenge in the field of microbiology despite countless attempts. Here, we conducted a comprehensive bibliographic analysis using several databases and search engines, namely Pubmed, Google scholar, Google, Web of Science and Scopus. Numerous unsuccessful empiric studies have been conducted and evaluated using as criteria dark-field microscopic observation of motile spiral shaped cells in the culture and virulence of the culture through rabbit infectivity. All of these studies failed to induce rabbit infectivity, even when deemed positive after microscopic observation leading to the misnomer of avirulent T. pallidum. In fact, this criterion was improperly chosen because not all spiral shaped cells are T. pallidum. However, these studies led to the formulation of culture media particularly favourable to the growth of several species of Treponema, including Oral Microbiology and Immunology, Zürich medium (OMIZ), Oral Treponeme Enrichment Broth (OTEB) and T-Raoult, thus allowing the increase in the number of cultivable strains of Treponema. The predicted metabolic capacities of T. pallidum show limited metabolism, also exhibited by other non-cultured and pathogenic Treponema species, in contrast to cultured Treponema species. The advent of next generation sequencing represents a turning point in this field, as the knowledge inferred from the genome can finally lead to the axenic culture of T. pallidum.
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Affiliation(s)
- Souad Belkacemi
- Aix-Marseille Univ, IRD, APHM, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection 19-21 Boulevard Jean Moulin 13005, Marseille, France
| | - Maryam Tidjani Alou
- Aix-Marseille Univ, IRD, APHM, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection 19-21 Boulevard Jean Moulin 13005, Marseille, France
| | - Saber Khelaifia
- Institut Hospitalo-Universitaire Méditerranée Infection 19-21 Boulevard Jean Moulin 13005, Marseille, France
| | - Didier Raoult
- Aix-Marseille Univ, IRD, APHM, MEPHI, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée Infection 19-21 Boulevard Jean Moulin 13005, Marseille, France
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8
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Yanez-Montalvo A, Gaona O, Águila B, Arias-Domínguez N, Falcón LI, Pérez-Flores J. Tapirus bairdii-Associated Fecal Microbiome from a Critical Conservation Area: Calakmul, México. Curr Microbiol 2021; 78:2648-2659. [PMID: 33990869 DOI: 10.1007/s00284-021-02531-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 05/03/2021] [Indexed: 11/28/2022]
Abstract
Baird's tapir (Tapirus bairdii) is the largest native terrestrial mammal in the Neotropics, which is endangered primarily as a consequence of habitat loss and overhunting. Baird's tapir is predominantly nocturnal and exists at low densities which complicates field studies. Baird's tapir is a large-bodied herbivore that plays a key role in maintaining healthy tropical forests through seed dispersal in its feces. Studies of gut microbiome are essential and valuable to assess the health status of the host and the interaction with the environment. In this study, we collected fresh fecal samples of T. bairdii to analyze its gut microbiome during the rainy and dry seasons in the Calakmul region, which is a critical rainforest conservation area in Mexico. The results of a high-throughput 16S rDNA gene sequencing approach suggest that the fecal microbiome of Baird's tapir has no significant differences in composition among seasons. The most common phyla were Firmicutes, Bacteroidetes, Proteobacteria, Kiritimatiellaeota, and Spirochaetes. This study suggests that the stability of the fecal microbiome is related to similar feeding strategies throughout the year, and emphasizes the value of tapir in seed dispersal (and associated microbes) to the well-conserved forests of the Greater Calakmul region as biodiversity hotspots for conservation.
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Affiliation(s)
- Alfredo Yanez-Montalvo
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, 97302, Mérida, México.,El Colegio de La Frontera Sur, Unidad de Chetumal, Avenida Centenario Km 5.5, 77014, Chetumal, Quintana Roo, México
| | - Osiris Gaona
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, 97302, Mérida, México
| | - Bernardo Águila
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, 97302, Mérida, México
| | | | - Luisa I Falcón
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, 97302, Mérida, México
| | - Jonathan Pérez-Flores
- El Colegio de La Frontera Sur, Unidad de Chetumal, Avenida Centenario Km 5.5, 77014, Chetumal, Quintana Roo, México. .,Universidad Tecnológica de Calakmul, Carretera Estatal Xpujil-Dzibalchen Km 2, 24640, Calakmul, Campeche, México.
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Staton GJ, Clegg SR, Ainsworth S, Armstrong S, Carter SD, Radford AD, Darby A, Wastling J, Hall N, Evans NJ. Dissecting the molecular diversity and commonality of bovine and human treponemes identifies key survival and adhesion mechanisms. PLoS Pathog 2021; 17:e1009464. [PMID: 33780514 PMCID: PMC8049484 DOI: 10.1371/journal.ppat.1009464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 04/15/2021] [Accepted: 03/10/2021] [Indexed: 12/13/2022] Open
Abstract
Here, we report the first complete genomes of three cultivable treponeme species from bovine digital dermatitis (DD) skin lesions, two comparative human treponemes, considered indistinguishable from bovine DD species, and a bovine gastrointestinal (GI) treponeme isolate. Key genomic differences between bovine and human treponemes implicate microbial mechanisms that enhance knowledge of how DD, a severe disease of ruminants, has emerged into a prolific, worldwide disease. Bovine DD treponemes have additional oxidative stress genes compared to nearest human-isolated relatives, suggesting better oxidative stress tolerance, and potentially explaining how bovine strains can colonize skin surfaces. Comparison of both bovine DD and GI treponemes as well as bovine pathogenic and human non-pathogenic saprophyte Treponema phagedenis strains indicates genes encoding a five-enzyme biosynthetic pathway for production of 2,3-diacetamido-2,3-dideoxy-d-mannuronic acid, a rare di-N-acetylated mannuronic acid sugar, as important for pathogenesis. Bovine T. phagedenis strains further differed from human strains by having unique genetic clusters including components of a type IV secretion system and a phosphate utilisation system including phoU, a gene associated with osmotic stress survival. Proteomic analyses confirmed bovine derived T. phagedenis exhibits expression of PhoU but not the putative secretion system, whilst the novel mannuronic acid pathway was expressed in near entirety across the DD treponemes. Analysis of osmotic stress response in water identified a difference between bovine and human T. phagedenis with bovine strains exhibiting enhanced survival. This novel mechanism could enable a selective advantage, allowing environmental persistence and transmission of bovine T. phagedenis. Finally, we investigated putative outer membrane protein (OMP) ortholog families across the DD treponemes and identified several families as multi-specific adhesins capable of binding extra cellular matrix (ECM) components. One bovine pathogen specific adhesin ortholog family showed considerable serodiagnostic potential with the Treponema medium representative demonstrating considerable disease specificity (91.6%). This work has shed light on treponeme host adaptation and has identified candidate molecules for future diagnostics, vaccination and therapeutic intervention.
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Affiliation(s)
- Gareth J. Staton
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Simon R. Clegg
- School of Life Sciences, College of Science, University of Lincoln, Brayford Pool Campus, Lincoln, United Kingdom
| | - Stuart Ainsworth
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Stuart Armstrong
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Stuart D. Carter
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Alan D. Radford
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Alistair Darby
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Jonathan Wastling
- Faculty of Natural Sciences, Keele University, Keele, Staffordshire, United Kingdom
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
- Department of Biological Sciences, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Nicholas J. Evans
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, United Kingdom
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10
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Newbrook K, Carter SD, Crosby-Durrani H, Evans NJ. Challenge of Bovine Foot Skin Fibroblasts With Digital Dermatitis Treponemes Identifies Distinct Pathogenic Mechanisms. Front Cell Infect Microbiol 2021; 10:538591. [PMID: 33489929 PMCID: PMC7820575 DOI: 10.3389/fcimb.2020.538591] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 11/24/2020] [Indexed: 11/13/2022] Open
Abstract
Bovine digital dermatitis (BDD) is a common infectious disease of digital skin in cattle and an important cause of lameness worldwide, with limited treatment options. It is of increasing global concern for both animal welfare and food security, imposing a large economic burden on cattle farming industries each year. A polytreponemal etiology has been consistently identified, with three key phylogroups implicated globally: Treponema medium, Treponema phagedenis, and Treponema pedis. Pathogenic mechanisms which might enable targeted treatment/therapeutic development are poorly defined. This study used RNA sequencing to determine global differential mRNA expression in primary bovine foot skin fibroblasts following challenge with three representative BDD treponemes and a commensal treponeme, Treponema ruminis. A pro-inflammatory response was elicited by the BDD treponemes, mediated through IL-8/IL-17 signaling. Unexpectedly, the three BDD treponemes elicited distinct mechanisms of pathogenesis. T. phagedenis and T. pedis increased abundance of mRNA transcripts associated with apoptosis, while T. medium and T. pedis increased transcripts involved in actin rearrangement and loss of cell adhesion, likely promoting tissue invasion. The upregulation of antimicrobial peptide precursor, DEFB123, by T. phagedenis spirochaetes may present a microbial ecological advantage to all treponemes within BDD infected tissue, explaining their dominance within lesions. A commensal, T. ruminis, significantly dysregulated over three times the number of host mRNA transcripts compared to BDD treponemes, implying BDD treponemes, akin to the syphilis pathogen (Treponema pallidum), have evolved as "stealth pathogens" which avoid triggering substantial host immune/inflammatory responses to enable persistence and tissue invasion. Immunohistochemistry demonstrated increased IL-6, IL-8, RND1, and CFB protein expression in BDD lesions, confirming in vitro fibroblast observations and highlighting the system's value in modeling BDD pathogenesis. Several unique shared gene targets were identified, particularly RGS16, GRO1, MAFF, and ZC3H12A. The three key BDD Treponema phylogroups elicited both distinct and shared pathogenic mechanisms in bovine foot skin; upregulating inflammation whilst simultaneously suppressing adaptive immunity. The novel gene targets identified here should enable future vaccine/therapeutic approaches.
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Affiliation(s)
- Kerry Newbrook
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Stuart D Carter
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Hayley Crosby-Durrani
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Nicholas J Evans
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
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11
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McLoughlin S, Spillane C, Claffey N, Smith PE, O’Rourke T, Diskin MG, Waters SM. Rumen Microbiome Composition Is Altered in Sheep Divergent in Feed Efficiency. Front Microbiol 2020; 11:1981. [PMID: 32983009 PMCID: PMC7477290 DOI: 10.3389/fmicb.2020.01981] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 07/27/2020] [Indexed: 12/19/2022] Open
Abstract
Rumen microbiome composition and functionality is linked to animal feed efficiency, particularly for bovine ruminants. To investigate this in sheep, we compared rumen bacterial and archaeal populations (and predicted metabolic processes) of sheep divergent for the feed efficiency trait feed conversion ratio (FCR). In our study 50 Texel cross Scottish Blackface (TXSB) ram lambs were selected from an original cohort of 200 lambs. From these, 26 were further selected for experimentation based on their extreme FCR (High Feed Efficiency, HFE = 13; Low Feed Efficiency, LFE = 13). Animals were fed a 95% concentrate diet ad libitum over 36 days. 16S rRNA amplicon sequencing was used to investigate the rumen bacterial and archaeal communities in the liquid and solid rumen fractions of sheep divergent for FCR. Weighted UniFrac distances separated HFE and LFE archaea communities from the liquid rumen fraction (Permanova, P < 0.05), with greater variation observed for the LFE cohort (Permdisp, P < 0.05). LFE animals exhibited greater Shannon and Simpson diversity indices, which was significant for the liquid rumen fraction (P < 0.05). Methanobrevibacter olleyae (in liquid and solid fractions) and Methanobrevibacter millerae (liquid fraction) were differentially abundant, and increased in the LFE cohort (P.adj < 0.05), while Methanobrevibacter wolinii (liquid fraction) was increased in the HFE cohort (P.adj < 0.05). This suggests that methanogenic archaea may be responsible for a potential loss of energy for the LFE cohort. Bacterial community composition (Permanova, P > 0.1) and diversity (P > 0.1) was not affected by the FCR phenotype. Only the genus Prevotella 1 was differentially abundant between HFE and LFE cohorts. Although no major compositional shifts of bacterial populations were identified amongst the feed efficient cohorts (FDR > 0.05), correlation analysis identified putative drivers of feed efficiency with Ruminococcaceae UCG-014 (liquid, rho = -0.53; solid, rho = -0.56) and Olsenella (solid, rho = -0.40) exhibiting significant negative association with FCR (P < 0.05). Bifidobacterium and Megasphaera showed significant positive correlations with ADG. Major cellulolytic bacteria Fibrobacter (liquid, rho = 0.43) and Ruminococcus 1 (liquid, rho = 0.41; solid, rho = 41) correlated positively with FCR (P < 0.05). Our study provides evidence that feed efficiency in sheep is likely influenced by compositional changes to the archaeal community, and abundance changes of specific bacteria, rather than major overall shifts within the rumen microbiome.
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Affiliation(s)
- Steven McLoughlin
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, Ireland
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Noel Claffey
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, Ireland
| | - Paul E. Smith
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, Ireland
| | - Tommy O’Rourke
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, Ireland
| | - Michael G. Diskin
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, Ireland
| | - Sinéad M. Waters
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, Ireland
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway, Ireland
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12
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Ribeiro GO, Gruninger RJ, Jones DR, Beauchemin KA, Yang WZ, Wang Y, Abbott DW, Tsang A, McAllister TA. Effect of ammonia fiber expansion-treated wheat straw and a recombinant fibrolytic enzyme on rumen microbiota and fermentation parameters, total tract digestibility, and performance of lambs. J Anim Sci 2020; 98:skaa116. [PMID: 32369600 PMCID: PMC7199887 DOI: 10.1093/jas/skaa116] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/28/2020] [Indexed: 12/30/2022] Open
Abstract
The objective of this study was to evaluate the effect of ammonia fiber expansion (AFEX)-treated wheat straw pellets and a recombinant fibrolytic enzyme on the rumen microbiome, rumen fermentation parameters, total tract diet digestibility, and performance of lambs. Eight rumen cannulated wethers and 60 lambs (n = 15 per diet, 8 rams and 7 ewes) were used in a replicated 4 × 4 Latin square design digestibility study and a complete randomized growth performance study, respectively. Four treatment diets were arranged in a 2 × 2 factorial structure with AFEX wheat straw (0% or 30% AFEX straw pellets on a dietary DM basis replacing alfalfa hay pellets) and fibrolytic enzyme (with or without XYL10C, a β-1,4-xylanase, from Aspergillus niger) as main factors. Enzyme was applied at 100 mg/kg of diet DM, 22 h before feeding. Rumen bacteria diversity Pielou evenness decreased (P = 0.05) with AFEX compared with the control diet and increased (P < 0.01) with enzyme. Enzyme increased (P ≤ 0.02) the relative abundancies of Prevotellaceae UCG-004, Christensenellaceae R-7 group, Saccharofermentans, and uncultured Kiritimatiellaeota. Total protozoa counts were greater (P ≤ 0.04) in the rumen of lambs fed AFEX compared with control, with enzyme reducing (P ≤ 0.05) protozoa counts for both diets. Digestibility of DM did not differ (P > 0.10) among diets, but digestibility of CP was reduced (P = 0.001), and digestibility of NDF and ADF increased (P < 0.05) as AFEX replaced alfalfa. Compared with control, AFEX promoted greater DMI (P = 0.003) and improved ADG up to 42 d on feed (P = 0.03), but not (P = 0.51) over the full ~94-d experiment. Consequently, overall G:F was reduced (P = 0.04) for AFEX when compared with control (0.188 vs. 0.199), but days on feed were lower (P = 0.04) for AFEX (97 vs. 91 d). Enzyme improved DMI of AFEX up to day 70 (P = 0.01), but did not affect DMI of the control diet. Enzyme addition improved ADG of lambs fed both diets in the first 28 d (P = 0.02), but not over the entire feeding period (P ≥ 10). As a result, G:F was improved with enzyme for the first 28 d (P = 0.04), but not overall (P = 0.45). This study shows that AFEX-treated wheat straw can replace alfalfa hay with no loss in lamb growth performance. Additionally, the enzyme XYL10C altered the rumen microbiome and improved G:F in the first month of the feeding.
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Affiliation(s)
- Gabriel O Ribeiro
- Department of Animal and Poultry Science, University of Saskatchewan College of Agriculture Bioresources, University of Saskatchewan, Saskatoon, Canada
| | - Robert J Gruninger
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - Darryl R Jones
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - Karen A Beauchemin
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - Wen Zhu Yang
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - Yuxi Wang
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - D Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
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13
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Macdonald SS, Armstrong Z, Morgan-Lang C, Osowiecka M, Robinson K, Hallam SJ, Withers SG. Development and Application of a High-Throughput Functional Metagenomic Screen for Glycoside Phosphorylases. Cell Chem Biol 2019; 26:1001-1012.e5. [PMID: 31080075 DOI: 10.1016/j.chembiol.2019.03.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/15/2019] [Accepted: 03/27/2019] [Indexed: 01/19/2023]
Abstract
Glycoside phosphorylases (GPs) catalyze the reversible phosphorolysis of glycosidic bonds, releasing sugar 1-phosphates. To identify a greater range of these under-appreciated enzymes, we have developed a high-throughput functional screening method based on molybdenum blue formation. In a proof-of-principle screen focused on cellulose-degrading GPs we interrogated ∼23,000 large insert (fosmid) clones sourced from microbial communities inhabiting two separate environments and identified seven novel GPs from carbohydrate active enzyme family GH94 and one from GH149. Characterization identified cellobiose phosphorylases, cellodextrin phosphorylases, laminaribiose phosphorylases, and a β-1,3-glucan phosphorylase. To demonstrate the versatility of the screening method, varying substrate combinations were used to identify GP activity from families GH13, GH65, GH112, and GH130 in addition to GH94 and GH149. These pilot screen and substrate versatility results provide a screening paradigm platform for recovering diverse GPs from uncultivated microbial communities acting on different substrates with considerable potential to unravel previously unknown degradative pathways within microbiomes.
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Affiliation(s)
- Spencer S Macdonald
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada; Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; ECOSCOPE Training Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Zachary Armstrong
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada; Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Connor Morgan-Lang
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Magdalena Osowiecka
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Kyle Robinson
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada; ECOSCOPE Training Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; ECOSCOPE Training Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada; Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; ECOSCOPE Training Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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14
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Staton GJ, Newbrook K, Clegg SR, Birtles RJ, Evans NJ, Carter SD. Treponema rectale sp. nov., a spirochete isolated from the bovine rectum. Int J Syst Evol Microbiol 2017; 67:2470-2475. [DOI: 10.1099/ijsem.0.002051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Gareth J. Staton
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, iC2 Building, Liverpool Science Park, Brownlow Hill, Liverpool, L3 5RF, UK
| | - Kerry Newbrook
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, iC2 Building, Liverpool Science Park, Brownlow Hill, Liverpool, L3 5RF, UK
| | - Simon R. Clegg
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, iC2 Building, Liverpool Science Park, Brownlow Hill, Liverpool, L3 5RF, UK
| | - Richard J. Birtles
- School of Environment and Life Sciences, Peel Building, University of Salford, Salford, M5 4WT, UK
| | - Nicholas J. Evans
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, iC2 Building, Liverpool Science Park, Brownlow Hill, Liverpool, L3 5RF, UK
| | - Stuart D. Carter
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, iC2 Building, Liverpool Science Park, Brownlow Hill, Liverpool, L3 5RF, UK
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