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Niu X, Lin L, Zhang T, An X, Li Y, Yu Y, Hong M, Shi H, Ding L. Comparison of the intestinal flora of wild and artificial breeding green turtles ( Chelonia mydas). Front Microbiol 2024; 15:1412015. [PMID: 38873159 PMCID: PMC11170157 DOI: 10.3389/fmicb.2024.1412015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 05/06/2024] [Indexed: 06/15/2024] Open
Abstract
Gut microbes are pivotal reference indicators for assessing the health status of animals. Before introducing artificially bred species into the wild, examining their gut microbe composition is crucial to help mitigate potential threats posed to wild populations. However, gut microbiological trait similarities between wild and artificially bred green turtles remain unexplored. Therefore, this study compared the gut microbiological characteristics of wild and artificially bred green turtles (Chelonia mydas) through high-throughput Illumina sequencing technology. The α-diversity of intestinal bacteria in wild green turtles, as determined by Shannon and Chao indices, significantly surpasses that of artificial breeding green turtles (p < 0.01). However, no significant differences were detected in the fungal α-diversity between wild and artificially bred green turtles. Meanwhile, the β-diversity analysis revealed significant differences between wild and artificially bred green turtles in bacterial and fungal compositions. The community of gut bacteria in artificially bred green turtles had a significantly higher abundance of Fusobacteriota including those belonging to the Paracoccus, Cetobacterium, and Fusobacterium genera than that of the wild green turtle. In contrast, the abundance of bacteria belonging to the phylum Actinobacteriota and genus Nautella significantly decreased. Regarding the fungal community, artificially bred green turtles had a significantly higher abundance of Fusarium, Sterigmatomyces, and Acremonium and a lower abundance of Candida and Rhodotorula than the wild green turtle. The PICRUSt2 analyses demonstrated significant differences in the functions of the gut bacterial flora between groups, particularly in carbohydrate and energy metabolism. Fungal functional guild analysis further revealed that the functions of the intestinal fungal flora of wild and artificially bred green turtles differed significantly in terms of animal pathogens-endophytes-lichen parasites-plant pathogens-soil saprotrophs-wood saprotrophs. BugBase analysis revealed significant potential pathogenicity and stress tolerance variations between wild and artificially bred green turtles. Collectively, this study elucidates the distinctive characteristics of gut microbiota in wild and artificially bred green turtles while evaluating their health status. These findings offer valuable scientific insights for releasing artificially bred green turtles and other artificially bred wildlife into natural habitats.
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Affiliation(s)
- Xin Niu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
- Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha, China
| | - Liu Lin
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
- Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha, China
| | - Ting Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
- Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha, China
| | - Xiaoyu An
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
- Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha, China
| | - Yupei Li
- Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha, China
- Marine Protected Area Administration of Sansha City, Sansha, China
| | - Yangfei Yu
- Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha, China
- Marine Protected Area Administration of Sansha City, Sansha, China
| | - Meiling Hong
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
- Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha, China
| | - Haitao Shi
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
- Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha, China
| | - Li Ding
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
- Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha, China
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Bouchali R, Mandon C, Danty-Berger E, Géloën A, Marjolet L, Youenou B, Pozzi ACM, Vareilles S, Galia W, Kouyi GL, Toussaint JY, Cournoyer B. Runoff microbiome quality assessment of a city center rainwater harvesting zone shows a differentiation of pathogen loads according to human mobility patterns. Int J Hyg Environ Health 2024; 260:114391. [PMID: 38781750 DOI: 10.1016/j.ijheh.2024.114391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 03/15/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024]
Abstract
The hygienic quality of urban surfaces can be impaired by multiple sources of microbiological contaminants. These surfaces can trigger the development of multiple bacterial taxa and favor their spread during rain events through the circulation of runoff waters. These runoff waters are commonly directed toward sewer networks, stormwater infiltration systems or detention tanks prior a release into natural water ways. With water scarcity becoming a major worldwide issue, these runoffs are representing an alternative supply for some usage like street cleaning and plant watering. Microbiological hazards associated with these urban runoffs, and surveillance guidelines must be defined to favor these uses. Runoff microbiological quality from a recently implemented city center rainwater harvesting zone was evaluated through classical fecal indicator bacteria (FIB) assays, quantitative PCR and DNA meta-barcoding analyses. The incidence of socio-urbanistic patterns on the organization of these urban microbiomes were investigated. FIB and DNA from Human-specific Bacteroidales and pathogens such as Staphylococcus aureus were detected from most runoffs and showed broad distribution patterns. 16S rRNA DNA meta-barcoding profilings further identified core recurrent taxa of health concerns like Acinetobacter, Mycobacterium, Aeromonas and Pseudomonas, and divided these communities according to two main groups of socio-urbanistic patterns. One of these was highly impacted by heavy traffic, and showed recurrent correlation networks involving bacterial hydrocarbon degraders harboring significant virulence properties. The tpm-based meta-barcoding approach identified some of these taxa at the species level for more than 30 genera. Among these, recurrent pathogens were recorded such as P. aeruginosa, P. paraeruginosa, and Aeromonas caviae. P. aeruginosa and A. caviae tpm reads were found evenly distributed over the study site but those of P. paraeruginosa were higher among sub-catchments impacted by heavy traffic. Health risks associated with these runoff P. paraeruginosa emerging pathogens were high and associated with strong cytotoxicity on A549 lung cells. Recurrent detections of pathogens in runoff waters highlight the need of a microbiological surveillance prior allowing their use. Good microbiological quality can be obtained for certain typologies of sub-catchments with good hygienic practices but not all. A reorganization of Human mobility and behaviors would likely trigger changes in these bacterial diversity patterns and reduce the occurrences of the most hazardous groups.
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Affiliation(s)
- Rayan Bouchali
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Claire Mandon
- Université de Lyon, INSA Lyon, UMR Environnement, Ville, Société, CNRS 5600, 18 rue Chevreul, 69362, Lyon, France
| | - Emmanuelle Danty-Berger
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Alain Géloën
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Laurence Marjolet
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Benjamin Youenou
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Adrien C M Pozzi
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Sophie Vareilles
- Université de Lyon, INSA Lyon, UMR Environnement, Ville, Société, CNRS 5600, 18 rue Chevreul, 69362, Lyon, France
| | - Wessam Galia
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | | | - Jean-Yves Toussaint
- Université de Lyon, INSA Lyon, UMR Environnement, Ville, Société, CNRS 5600, 18 rue Chevreul, 69362, Lyon, France
| | - Benoit Cournoyer
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France.
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Visser AN, Martin JD, Osenbrück K, Rügner H, Grathwohl P, Kappler A. In situ incubation of iron(II)-bearing minerals and Fe(0) reveals insights into metabolic flexibility of chemolithotrophic bacteria in a nitrate polluted karst aquifer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:172062. [PMID: 38554974 DOI: 10.1016/j.scitotenv.2024.172062] [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: 12/04/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
Groundwater nitrate pollution is a major reason for deteriorating water quality and threatens human and animal health. Yet, mitigating groundwater contamination naturally is often complicated since most aquifers are limited in bioavailable carbon. Since metabolically flexible microbes might have advantages for survival, this study presents a detailed description and first results on our modification of the BacTrap© method, aiming to determine the prevailing microbial community's potential to utilize chemolithotrophic pathways. Our microbial trapping devices (MTDs) were amended with four different iron sources and incubated in seven groundwater monitoring wells for ∼3 months to promote growth of nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOxB) in a nitrate-contaminated karst aquifer. Phylogenetic analysis based on 16S rRNA gene sequences implies that the identity of the iron source influenced the microbial community's composition. In addition, high throughput amplicon sequencing revealed increased relative 16S rRNA gene abundances of OTUs affiliated to genera such as Thiobacillus, Rhodobacter, Pseudomonas, Albidiferax, and Sideroxydans. MTD-derived enrichments set up with Fe(II)/nitrate/acetate to isolate potential NRFeOxB, were dominated by e.g., Acidovorax spp., Paracoccus spp. and Propionivibrio spp. MTDs are a cost-effective approach for investigating microorganisms in groundwater and our data not only solidifies the MTD's capacity to provide insights into the metabolic flexibility of the aquifer's microbial community, but also substantiates its metabolic potential for anaerobic Fe(II) oxidation.
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Affiliation(s)
- Anna-Neva Visser
- GeoZentrum Nordbayern, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Germany; Department of Geosciences, University of Tübingen, Germany.
| | - Joseph D Martin
- Department of Biology, Terrestrial Ecology, University of Copenhagen, Denmark
| | - Karsten Osenbrück
- Department of Geosciences, University of Tübingen, Germany; Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | - Hermann Rügner
- Department of Geosciences, University of Tübingen, Germany
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Branysova T, Petru N, Lopez Marin MA, Solcova M, Demnerova K, Stiborova H. Uncovering the microbial diversity of Czech Republic archives: A study of metabolically active airborne microbes. Heliyon 2024; 10:e27930. [PMID: 38560214 PMCID: PMC10981025 DOI: 10.1016/j.heliyon.2024.e27930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/23/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
Despite the diligent efforts of libraries, archives, and similar institutions to preserve cultural monuments, biodeterioration continues to pose a significant threat to these objects. One of the main sources of microorganisms responsible for the biodeterioration process is the presence of airborne microorganisms. Therefore, this research aims to monitor and compare outcomes of both culture-dependent (utilising various cultivation strategies) and culture-independent approaches (RNA-based sequencing) to identifying metabolically active airborne microorganisms in archives in the Czech Republic. Through this study, several species that have the potential to pose risks to both cultural heritage objects and the health of institution employees were found. Additionally, the efficacy of different cultivation media was demonstrated to be varied across archive rooms, highlighting the necessity of employing multiple cultivation media for comprehensive analyses. Of noteworthy importance, the resuscitating-promoting factor (Rpf) proved to be a pivotal tool, increasing bacterial culturability by up to 30% when synergistically employed Reasoner's 2A agar (R2A) and R2A + Rpf media. Next, the study emphasises the importance of integrating both culture-dependent and culture-independent approaches. The overlap between genera identified by the culture-dependent approach and those identified also by the culture-independent approach varied from 33% to surpassing 94%, with the maximum alignment exceeding 94% in only one case. Our results highlight the importance of actively monitoring and assessing levels of microbial air contamination in archives to prevent further deterioration of cultural heritage objects and to promote improved conditions for employees in archives and similar institutions.
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Affiliation(s)
- Tereza Branysova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 166 28, Prague, Czech Republic
| | - Nicole Petru
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 166 28, Prague, Czech Republic
| | - Marco A. Lopez Marin
- Department of Water Technology and Environmental Engineering, Faculty of Environmental Technology, University of Chemistry and Technology, Technicka 3, 166 28, Prague, Czech Republic
| | - Milada Solcova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 166 28, Prague, Czech Republic
| | - Katerina Demnerova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 166 28, Prague, Czech Republic
| | - Hana Stiborova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 166 28, Prague, Czech Republic
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Zhao Y, Li X, Bao H, Nan J. Effects of biochar-derived dissolved organic matter on the gut microbiomes and metabolomics in earthworm Eisenia fetida. ENVIRONMENTAL RESEARCH 2024; 245:117932. [PMID: 38104913 DOI: 10.1016/j.envres.2023.117932] [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: 10/22/2023] [Revised: 12/06/2023] [Accepted: 12/10/2023] [Indexed: 12/19/2023]
Abstract
The ecological risks of biochar-derived dissolved organic matter (DOM) to soil invertebrates at different organismal levels remains limited. This study comprehensively explored the ecological risks of biochar-derived DOM on earthworm gut through assessments of enzyme activity response, histopathology, gut microbiomes, and metabolomics. Results demonstrated that DOM disturbed the digestive enzymes in earthworm, especially for 10% DOM300 groups. The integrated biomarker response v2 (IBRv2) indicated that the perturbation of earthworm digestive enzymes induced by DOM was both time-dependent and dose-dependent. Pathological observations revealed that 10% DOM300 damaged intestinal epithelium and digestive lumen of earthworms. The significant damage and injury to earthworms caused by DOM300 due to its higher concentrations of heavy metal ions and organic substrates (e.g., toluene, hexane, butanamide, and hexanamide) compared to DOM500 and DOM700. Analysis of 16S rRNA from the gut microbiota showed a significant decrease in genera (Verminephrobacter, Bacillus, and Microbacteriaceae) associated with inflammation, disease, and detoxification processes. Furthermore, 10% DOM300 caused the abnormality of metabolites, such as glutamate, fumaric acid, pyruvate, and citric acid, which were involved in energy metabolism, These findings contributed to improve our understanding of the toxic mechanism of biochar DOM from multiple perspectives.
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Affiliation(s)
- Yue Zhao
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Xin Li
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China.
| | - Huanyu Bao
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Jun Nan
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China
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Pal U, Bachmann D, Pelzer C, Christiansen J, Blank LM, Tiso T. A genetic toolbox to empower Paracoccus pantotrophus DSM 2944 as a metabolically versatile SynBio chassis. Microb Cell Fact 2024; 23:53. [PMID: 38360576 PMCID: PMC10870620 DOI: 10.1186/s12934-024-02325-0] [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: 01/12/2024] [Accepted: 02/05/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND To contribute to the discovery of new microbial strains with metabolic and physiological robustness and develop them into successful chasses, Paracoccus pantotrophus DSM 2944, a Gram-negative bacterium from the phylum Alphaproteobacteria and the family Rhodobacteraceae, was chosen. The strain possesses an innate ability to tolerate high salt concentrations. It utilizes diverse substrates, including cheap and renewable feedstocks, such as C1 and C2 compounds. Also, it can consume short-chain alkanes, predominately found in hydrocarbon-rich environments, making it a potential bioremediation agent. The demonstrated metabolic versatility, coupled with the synthesis of the biodegradable polymer polyhydroxyalkanoate, positions this microbial strain as a noteworthy candidate for advancing the principles of a circular bioeconomy. RESULTS The study aims to follow the chassis roadmap, as depicted by Calero and Nikel, and de Lorenzo, to transform wild-type P. pantotrophus DSM 2944 into a proficient SynBio (Synthetic Biology) chassis. The initial findings highlight the antibiotic resistance profile of this prospective SynBio chassis. Subsequently, the best origin of replication (ori) was identified as RK2. In contrast, the non-replicative ori R6K was selected for the development of a suicide plasmid necessary for genome integration or gene deletion. Moreover, when assessing the most effective method for gene transfer, it was observed that conjugation had superior efficiency compared to electroporation, while transformation by heat shock was ineffective. Robust host fitness was demonstrated by stable plasmid maintenance, while standardized gene expression using an array of synthetic promoters could be shown. pEMG-based scarless gene deletion was successfully adapted, allowing gene deletion and integration. The successful integration of a gene cassette for terephthalic acid degradation is showcased. The resulting strain can grow on both monomers of polyethylene terephthalate (PET), with an increased growth rate achieved through adaptive laboratory evolution. CONCLUSION The chassis roadmap for the development of P. pantotrophus DSM 2944 into a proficient SynBio chassis was implemented. The presented genetic toolkit allows genome editing and therewith the possibility to exploit Paracoccus for a myriad of applications.
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Affiliation(s)
- Upasana Pal
- Institute of Applied Microbiology, RWTH Aachen University, Aachen, Germany
| | - Denise Bachmann
- Institute of Applied Microbiology, RWTH Aachen University, Aachen, Germany
| | - Chiara Pelzer
- Institute of Applied Microbiology, RWTH Aachen University, Aachen, Germany
| | - Julia Christiansen
- Institute of Applied Microbiology, RWTH Aachen University, Aachen, Germany
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | - Lars M Blank
- Institute of Applied Microbiology, RWTH Aachen University, Aachen, Germany
| | - Till Tiso
- Institute of Applied Microbiology, RWTH Aachen University, Aachen, Germany.
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Hollensteiner J, Schneider D, Poehlein A, Brinkhoff T, Daniel R. Pan-genome analysis of six Paracoccus type strain genomes reveal lifestyle traits. PLoS One 2023; 18:e0287947. [PMID: 38117845 PMCID: PMC10732464 DOI: 10.1371/journal.pone.0287947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 11/15/2023] [Indexed: 12/22/2023] Open
Abstract
The genus Paracoccus capable of inhabiting a variety of different ecological niches both, marine and terrestrial, is globally distributed. In addition, Paracoccus is taxonomically, metabolically and regarding lifestyle highly diverse. Until now, little is known on how Paracoccus can adapt to such a range of different ecological niches and lifestyles. In the present study, the genus Paracoccus was phylogenomically analyzed (n = 160) and revisited, allowing species level classification of 16 so far unclassified Paracoccus sp. strains and detection of five misclassifications. Moreover, we performed pan-genome analysis of Paracoccus-type strains, isolated from a variety of ecological niches, including different soils, tidal flat sediment, host association such as the bluespotted cornetfish, Bugula plumosa, and the reef-building coral Stylophora pistillata to elucidate either i) the importance of lifestyle and adaptation potential, and ii) the role of the genomic equipment and niche adaptation potential. Six complete genomes were de novo hybrid assembled using a combination of short and long-read technologies. These Paracoccus genomes increase the number of completely closed high-quality genomes of type strains from 15 to 21. Pan-genome analysis revealed an open pan-genome composed of 13,819 genes with a minimal chromosomal core (8.84%) highlighting the genomic adaptation potential and the huge impact of extra-chromosomal elements. All genomes are shaped by the acquisition of various mobile genetic elements including genomic islands, prophages, transposases, and insertion sequences emphasizing their genomic plasticity. In terms of lifestyle, each mobile genetic elements should be evaluated separately with respect to the ecological context. Free-living genomes, in contrast to host-associated, tend to comprise (1) larger genomes, or the highest number of extra-chromosomal elements, (2) higher number of genomic islands and insertion sequence elements, and (3) a lower number of intact prophage regions. Regarding lifestyle adaptations, free-living genomes share genes linked to genetic exchange via T4SS, especially relevant for Paracoccus, known for their numerous extrachromosomal elements, enabling adaptation to dynamic environments. Conversely, host-associated genomes feature diverse genes involved in molecule transport, cell wall modification, attachment, stress protection, DNA repair, carbon, and nitrogen metabolism. Due to the vast number of adaptive genes, Paracoccus can quickly adapt to changing environmental conditions.
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Affiliation(s)
- Jacqueline Hollensteiner
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
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Sakda P, Xiang X, Song Z, Wu Y, Zhou L. Impact of Season on Intestinal Bacterial Communities and Pathogenic Diversity in Two Captive Duck Species. Animals (Basel) 2023; 13:3879. [PMID: 38136916 PMCID: PMC10740475 DOI: 10.3390/ani13243879] [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: 11/01/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Vertebrates and their gut bacteria interact in complex and mutually beneficial ways. The intestinal microbial composition is influenced by several external influences. In addition to food, the abiotic elements of the environment, such as temperature, humidity, and seasonal fluctuation are also important determinants. Fecal samples were collected from two captive duck species, Baikal teal (Sibirionetta formosa) and common teal (Anas crecca) across four seasons (summer, autumn, winter, and spring). These ducks were consistently fed the same diet throughout the entire experiment. High throughput sequencing (Illumina Mi-seq) was employed to analyze the V4-V5 region of the 16sRNA gene. The dominant phyla in all seasons were Proteobacteria and Firmicutes. Interestingly, the alpha diversity was higher in winter for both species. The NMDS, PCoA, and ANOSIM analysis showed the distinct clustering of bacterial composition between different seasons, while no significant differences were discovered between duck species within the same season. In addition, LefSe analysis demonstrated specific biomarkers in different seasons, with the highest number revealed in winter. The co-occurrence network analysis also showed that during winter, the network illustrated a more intricate structure with the greatest number of nodes and edges. However, this study identified ten potentially pathogenic bacterial species, which showed significantly enhanced diversity and abundance throughout the summer. Overall, our results revealed that season mainly regulated the intestinal bacterial community composition and pathogenic bacteria of captive ducks under the instant diet. This study provides an important new understanding of the seasonal variations in captive wild ducks' intestinal bacterial community structure. The information available here may be essential data for preventing and controlling infections caused by pathogenic bacteria in captive waterbirds.
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Affiliation(s)
- Patthanan Sakda
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (P.S.); (Z.S.); (Y.W.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei 230601, China
| | - Xingjia Xiang
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (P.S.); (Z.S.); (Y.W.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei 230601, China
- Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Chizhou 247230, China
| | - Zhongqiao Song
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (P.S.); (Z.S.); (Y.W.)
| | - Yuannuo Wu
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (P.S.); (Z.S.); (Y.W.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei 230601, China
| | - Lizhi Zhou
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (P.S.); (Z.S.); (Y.W.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei 230601, China
- Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Chizhou 247230, China
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Maurya S, Arya CK, Parmar N, Sathyanarayanan N, Joshi CG, Ramanathan G. Genomic profiling and characteristics of a C1 degrading heterotrophic fresh-water bacterium Paracoccus sp. strain DMF. Arch Microbiol 2023; 206:6. [PMID: 38015256 DOI: 10.1007/s00203-023-03729-z] [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: 03/31/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
Paracoccus species are metabolically versatile gram-negative, aerobic facultative methylotrophic bacteria showing enormous promise for environmental and bioremediation studies. Here we report, the complete genome analysis of Paracoccus sp. strain DMF (P. DMF) that was isolated from a domestic wastewater treatment plant in Kanpur, India (26.4287 °N, 80.3891 °E) based on its ability to degrade a recalcitrant organic solvent N, N-dimethylformamide (DMF). The results reveal a genome size of 4,202,269 base pairs (bp) with a G + C content of 67.9%. The assembled genome comprises 4141 coding sequences (CDS), 46 RNA sequences, and 2 CRISPRs. Interestingly, catabolic operons related to the conventional marine-based methylated amines (MAs) degradation pathway were functionally annotated within the genome of an obligated aerobic heterotroph that is P. DMF. The genomic data-based characterization presented here for the novel heterotroph P. DMF aims to improve the understanding of the phenotypic gene products, enzymes, and pathways involved with greater emphasis on facultative methylotrophic motility-based latent pathogenicity.
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Affiliation(s)
- Shiwangi Maurya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Chetan Kumar Arya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Nidhi Parmar
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382 011, India
| | - Nitish Sathyanarayanan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, 560065, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382 011, India
| | - Gurunath Ramanathan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India.
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10
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Tongsri P, Cheng G, Huang Z, Wang Z, Dong F, Wu Z, Kong W, Yu Y, Xu Z. Mucosal immunity and microbiota change in the rainbow trout (Oncorhynchus mykiss) gills after being challenged with infectious hematopoietic necrosis virus. FISH & SHELLFISH IMMUNOLOGY 2023; 142:109166. [PMID: 37844853 DOI: 10.1016/j.fsi.2023.109166] [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: 06/11/2023] [Revised: 09/19/2023] [Accepted: 10/14/2023] [Indexed: 10/18/2023]
Abstract
Respiratory structures are crucial for vertebrate survival, as they serve not only to perform gas-exchange processes but also as entry points for opportunistic pathogens. Previous studies have demonstrated that fish contain gill mucosal-associated lymphoid tissue, and harbor a large number of commensal bacteria on their surface and contribute to maintaining fish health. However, by far, very limited information is known regarding the effects of viral infection on gill mucosal immunity and microbiota homeostasis. In this study, we conducted an infection model by bath with infectious hematopoietic necrosis virus (IHNV) and revealed a 27 % mortality rate among rainbow trout in the first two weeks after infection. Moreover, we found that diseased fish with the highest IHNV loads in gills exhibiting severe damage, as well as increased goblet cell counts in both primary lamellae (PL) and secondary lamellae (SL). Additionally, RT-qPCR and RNA-seq analyses revealed that IHNV infection induced a strong innate and adaptive antiviral immune responses. Interestingly, an antibacterial immune response was also observed, suggesting that a secondary bacterial infection occurred in trout gills after viral infection. Furthermore, 16S rRNA analysis of trout gills revealed a profound dysbiosis marked by a loss of beneficial taxa and expansion of pathobionts following IHNV infection. Overall, our finding demonstrates that IHNV infection induces significant changes of the microbial community in the fish respiratory surface, thus triggering local antiviral and bacterial mucosal immunity.
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Affiliation(s)
- Pajongjit Tongsri
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Gaofeng Cheng
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zhenyu Huang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zixuan Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fen Dong
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zhengben Wu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Weiguang Kong
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yongyao Yu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zhen Xu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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11
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Staude B, Gschwendtner S, Frodermann T, Oehmke F, Kohl T, Kublik S, Schloter M, Ehrhardt H. Microbial signatures in amniotic fluid at preterm birth and association with bronchopulmonary dysplasia. Respir Res 2023; 24:248. [PMID: 37845700 PMCID: PMC10577941 DOI: 10.1186/s12931-023-02560-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/09/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND Microbiome dysbiosis can have long-lasting effects on our health and induce the development of various diseases. Bronchopulmonary dysplasia (BPD) is a multifactorial disease with pre- and postnatal origins including intra-amniotic infection as main risk factor. Recently, postnatal pathologic lung microbiota colonization was associated with BPD. The objectives of this prospective observational cohort study were to describe differences in bacterial signatures in the amniotic fluid (AF) of intact pregnancies without clinical signs or risk of preterm delivery and AF samples obtained during preterm deliveries and their variations between different BPD disease severity stages. METHODS AF samples were collected under sterile conditions during fetal intervention from intact pregnancies (n = 17) or immediately before preterm delivery < 32 weeks (n = 126). Metabarcoding based approaches were used for the molecular assessment of bacterial 16S rRNA genes to describe bacterial community structure. RESULTS The absolute amount of 16S rRNA genes was significantly increased in AF of preterm deliveries and detailed profiling revealed a reduced alpha diversity and a significant change in beta diversity with a reduced relative abundance of 16S rRNA genes indicative for Lactobacillus and Acetobacter while Fusobacterium, Pseudomonas, Ureaplasma and Staphylococcus 16S rRNA gene prevailed. Although classification of BPD by disease severity revealed equivalent absolute 16S rRNA gene abundance and alpha and beta diversity in no, mild and moderate/severe BPD groups, for some 16S rRNA genes differences were observed in AF samples. Bacterial signatures of infants with moderate/severe BPD showed predominance of 16S rRNA genes belonging to the Escherichia-Shigella cluster while Ureaplasma and Enterococcus species were enriched in AF samples of infants with mild BPD. CONCLUSIONS Our study identified distinct and diverse intrauterine 16S rRNA gene patterns in preterm infants immediately before birth, differing from the 16S rRNA gene signature of intact pregnancies. The distinct 16S rRNA gene signatures at birth derive from bacteria with varying pathogenicity to the immature lung and are suited to identify preterm infants at risk. Our results emphasize the prenatal impact to the origins of BPD.
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Affiliation(s)
- Birte Staude
- Department of General Pediatrics and Neonatology, Justus Liebig University and Universities of Giessen and Marburg Lung Center, Giessen, Germany
- German Center for Lung Research (DZL), Giessen, Germany
| | - Silvia Gschwendtner
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Tina Frodermann
- Department of General Pediatrics and Neonatology, Justus Liebig University and Universities of Giessen and Marburg Lung Center, Giessen, Germany
| | - Frank Oehmke
- Department of Gynecology and Obstetrics, Justus Liebig University of Giessen, Giessen, Germany
| | - Thomas Kohl
- Department of Gynecology and Obstetrics, Justus Liebig University of Giessen, Giessen, Germany
- German Center for Fetal Surgery and Minimally Invasive Therapy (DZFT), University of Mannheim (UMM), Mannheim, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Harald Ehrhardt
- Department of General Pediatrics and Neonatology, Justus Liebig University and Universities of Giessen and Marburg Lung Center, Giessen, Germany
- German Center for Lung Research (DZL), Giessen, Germany
- Division of Neonatology and Pediatric Intensive Care Medicine, Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
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12
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Hernandez-Leyva AJ, Rosen AL, Tomera CP, Lin EE, Akaho EH, Blatz AM, Otto WR, Logan J, Young LR, Harris RM, Kau AL, John ARO. Developmental progression of the nasopharyngeal microbiome during childhood and association with the lower airway microbiome. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.18.23295747. [PMID: 37790477 PMCID: PMC10543049 DOI: 10.1101/2023.09.18.23295747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Background The upper (URT) and lower (LRT) respiratory tract feature distinct environments and responses affecting microbial colonization but investigating the relationship between them is technically challenging. We aimed to identify relationships between taxa colonizing the URT and LRT and explore their relationship with development during childhood. Methods We employed V4 16S rDNA sequencing to profile nasopharyngeal swabs and tracheal aspirates collected from 183 subjects between 20 weeks and 18 years of age. These samples were collected prior to elective procedures at the Children's Hospital of Philadelphia over the course of 20 weeks in 2020, from otherwise healthy subjects enrolled in a study investigating potential reservoirs of SARS-CoV-2. Findings After extraction, sequencing, and quality control, we studied the remaining 124 nasopharyngeal swabs and 98 tracheal aspirates, including 85 subject-matched pairs of samples. V4 16S rDNA sequencing revealed that the nasopharynx is colonized by few, highly-abundant taxa, while the tracheal aspirates feature a diverse assembly of microbes. While no taxa co-occur in the URT and LRT of the same subject, clusters of microbiomes in the URT correlate with clusters of microbiomes in the LRT. The clusters identified in the URT correlate with subject age across childhood development. Interpretations The correlation between clusters of taxa across sites may suggest a mutual influence from either a third site, such as the oropharynx, or host-extrinsic, environmental features. The identification of a pattern of upper respiratory microbiota development across the first 18 years of life suggests that the patterns observed in early childhood may extend beyond the early life window.
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Affiliation(s)
- Ariel J Hernandez-Leyva
- Division of Allergy and Immunology, Department of Medicine and Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Anne L Rosen
- Division of Allergy and Immunology, Department of Medicine and Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Christopher P Tomera
- Division of Allergy and Immunology, Department of Medicine and Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Elaina E Lin
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Anesthesiology and Critical Care Medicine, Children's Hospital of Philadelphia, Philadelphia PA
| | - Elikplim H Akaho
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia PA
- Department of Medicine, John H. Stroger, Jr. Hospital of Cook County
| | - Allison M Blatz
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia PA
- Division of Critical Care Medicine, Department of Pediatrics, Nemours Children's Hospital, Wilmington DE
| | - William R Otto
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia PA
- Division of Infectious Disease, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Joey Logan
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia PA
| | - Lisa R Young
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia PA
| | - Rebecca M Harris
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia PA
| | - Andrew L Kau
- Division of Allergy and Immunology, Department of Medicine and Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Audrey R Odom John
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia PA
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13
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Szulc J, Okrasa M, Ryngajłło M, Pielech-Przybylska K, Gutarowska B. Markers of Chemical and Microbiological Contamination of the Air in the Sport Centers. Molecules 2023; 28:molecules28083560. [PMID: 37110794 PMCID: PMC10144153 DOI: 10.3390/molecules28083560] [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: 03/27/2023] [Revised: 04/11/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
This study aimed to assess the markers of chemical and microbiological contamination of the air at sport centers (e.g., the fitness center in Poland) including the determination of particulate matter, CO2, formaldehyde (DustTrak™ DRX Aerosol Monitor; Multi-functional Air Quality Detector), volatile organic compound (VOC) concentration (headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry), the number of microorganisms in the air (culture methods), and microbial biodiversity (high-throughput sequencing on the Illumina platform). Additionally the number of microorganisms and the presence of SARS-CoV-2 (PCR) on the surfaces was determined. Total particle concentration varied between 0.0445 mg m-3 and 0.0841 mg m-3 with the dominance (99.65-99.99%) of the PM2.5 fraction. The CO2 concentration ranged from 800 ppm to 2198 ppm, while the formaldehyde concentration was from 0.005 mg/m3 to 0.049 mg m-3. A total of 84 VOCs were identified in the air collected from the gym. Phenol, D-limonene, toluene, and 2-ethyl-1-hexanol dominated in the air at the tested facilities. The average daily number of bacteria was 7.17 × 102 CFU m-3-1.68 × 103 CFU m-3, while the number of fungi was 3.03 × 103 CFU m-3-7.34 × 103 CFU m-3. In total, 422 genera of bacteria and 408 genera of fungi representing 21 and 11 phyla, respectively, were detected in the gym. The most abundant bacteria and fungi (>1%) that belonged to the second and third groups of health hazards were: Escherichia-Shigella, Corynebacterium, Bacillus, Staphylococcus, Cladosporium, Aspergillus, and Penicillium. In addition, other species that may be allergenic (Epicoccum) or infectious (Acinetobacter, Sphingomonas, Sporobolomyces) were present in the air. Moreover, the SARS-CoV-2 virus was detected on surfaces in the gym. The monitoring proposal for the assessment of the air quality at a sport center includes the following markers: total particle concentration with the PM2.5 fraction, CO2 concentration, VOCs (phenol, toluene, and 2-ethyl-1-hexanol), and the number of bacteria and fungi.
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Affiliation(s)
- Justyna Szulc
- Department of Environmental Biotechnology, Lodz University of Technology, 90-530 Łódź, Poland
| | - Małgorzata Okrasa
- Department of Personal Protective Equipment, Central Institute for Labour Protection-National Research Institute, 90-133 Łódź, Poland
| | - Małgorzata Ryngajłło
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, 90-573 Łódź, Poland
| | | | - Beata Gutarowska
- Department of Environmental Biotechnology, Lodz University of Technology, 90-530 Łódź, Poland
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14
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Grandi G, Chiappa G, Ullman K, Lindgren PE, Olivieri E, Sassera D, Östlund E, Omazic A, Perissinotto D, Söderlund R. Characterization of the bacterial microbiome of Swedish ticks through 16S rRNA amplicon sequencing of whole ticks and of individual tick organs. Parasit Vectors 2023; 16:39. [PMID: 36717919 PMCID: PMC9885626 DOI: 10.1186/s13071-022-05638-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/24/2022] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND The composition of the microbial flora associated with ixodid ticks has been studied in several species, revealing the importance of geographical origin, developmental stage(s) and feeding status of the tick, as well as substantial differences between tissues and organs. Studying the microbiome in the correct context and scale is therefore necessary for understanding the interactions between tick-borne pathogens and other microorganisms as well as other aspects of tick biology. METHODS In the present study the microbial flora of whole Ixodes ricinus, I. persulcatus and I. trianguliceps ticks were analyzed with 16S rRNA amplicon sequencing. Additionally, tick organs (midguts, Malpighian tubules, ovaries, salivary glands) from flat and engorged I. ricinus female ticks were examined with the same methodology. RESULTS The most abundant bacteria belonged to the group of Proteobacteria (Cand. Midichloria mitochondrii and Cand. Lariskella). 16S amplicon sequencing of dissected tick organs provided more information on the diversity of I. ricinus-associated microbial flora, especially when organs were collected from engorged ticks. Bacterial genera significantly associated with tick feeding status as well as genera associated with the presence of tick-borne pathogens were identified. CONCLUSIONS These results contribute to the knowledge of microbial flora associated with ixodid ticks in their northernmost distribution limit in Europe and opens new perspectives for other investigations on the function of these bacteria, including those using other approaches like in vitro cultivation and in vitro models.
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Affiliation(s)
- Giulio Grandi
- grid.419788.b0000 0001 2166 9211Department of Microbiology, National Veterinary Institute (SVA), 751 89 Uppsala, Sweden ,grid.6341.00000 0000 8578 2742Department of Biomedical Sciences and Veterinary Public Health (BVF), Swedish University of Agricultural Sciences (SLU), Ulls Väg 26, 750 07 Uppsala, Sweden
| | - Giulia Chiappa
- grid.419788.b0000 0001 2166 9211Department of Microbiology, National Veterinary Institute (SVA), 751 89 Uppsala, Sweden
| | - Karin Ullman
- grid.419788.b0000 0001 2166 9211Department of Microbiology, National Veterinary Institute (SVA), 751 89 Uppsala, Sweden
| | - Per-Eric Lindgren
- grid.5640.70000 0001 2162 9922Department of Biomedical and Clinical Sciences, Division of Inflammation and Infection, Linköping University, 581 85 Linköping, Sweden ,grid.413253.2Department of Clinical Microbiology, County Hospital Ryhov, 551 85 Jönköping, Sweden
| | - Emanuela Olivieri
- grid.419583.20000 0004 1757 1598Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Strada Campeggi, 59/61, 27100 Pavia, Italy
| | - Davide Sassera
- grid.8982.b0000 0004 1762 5736Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Emma Östlund
- grid.419788.b0000 0001 2166 9211Department of Microbiology, National Veterinary Institute (SVA), 751 89 Uppsala, Sweden
| | - Anna Omazic
- grid.419788.b0000 0001 2166 9211Department of Chemistry, Environment, and Feed Hygiene, National Veterinary Institute (SVA), 751 89 Uppsala, Sweden
| | - Debora Perissinotto
- grid.419788.b0000 0001 2166 9211Department of Microbiology, National Veterinary Institute (SVA), 751 89 Uppsala, Sweden
| | - Robert Söderlund
- grid.419788.b0000 0001 2166 9211Department of Microbiology, National Veterinary Institute (SVA), 751 89 Uppsala, Sweden
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15
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Metaproteomic Analysis of an Oral Squamous Cell Carcinoma Dataset Suggests Diagnostic Potential of the Mycobiome. Int J Mol Sci 2023; 24:ijms24021050. [PMID: 36674563 PMCID: PMC9865486 DOI: 10.3390/ijms24021050] [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: 10/28/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 01/07/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most common head and neck malignancy, with an estimated 5-year survival rate of only 40-50%, largely due to late detection and diagnosis. Emerging evidence suggests that the human microbiome may be implicated in OSCC, with oral microbiome studies putatively identifying relevant bacterial species. As the impact of other microbial organisms, such as fungi and viruses, has largely been neglected, a bioinformatic approach utilizing the Trans-Proteomic Pipeline (TPP) and the R statistical programming language was implemented here to investigate not only bacteria, but also viruses and fungi in the context of a publicly available, OSCC, mass spectrometry (MS) dataset. Overall viral, bacterial, and fungal composition was inferred in control and OSCC patient tissue from protein data, with a range of proteins observed to be differentially enriched between healthy and OSCC conditions, of which the fungal protein profile presented as the best potential discriminator of OSCC within the analysed dataset. While the current project sheds new light on the fungal and viral spheres of the oral microbiome in cancer in silico, further research will be required to validate these findings in an experimental setting.
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16
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Schambach JY, Kruse CPS, Kitin P, Mays W, Hunt CG, Starkenburg SR, Barry AN. Metabolism of Scenedesmus obliquus cultivated with raw plant substrates. FRONTIERS IN PLANT SCIENCE 2022; 13:992702. [PMID: 36531386 PMCID: PMC9757167 DOI: 10.3389/fpls.2022.992702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/12/2022] [Indexed: 06/17/2023]
Abstract
The potential benefits of adding raw, non-food, lignocellulosic plant material as a carbon source for mixotrophic growth of microalgae have previously been demonstrated. This approach has advantages over using traditional carbon sources like glucose or acetate due to wide-spread plant biomass availability and substrate recalcitrance to bacterial contamination. Here, we report the overall growth characteristics and explore the metabolic patterns of Scenedesmus obliquus cultured in the presence raw plant substrate. An initial screen of plant substrate candidates showed an increase in specific growth rate and biomass accumulation when S. obliquus was cultured in the presence of switchgrass or yard waste compared to media alone. We observed a near doubling of microalgal dry weight when S. obliquus was grown with 0.2% (w/v) switchgrass under ambient CO2. Scanning electron microscopy (SEM) of corn stem after S. obliquus cultivation exhibited substantial phloem degradation. Transcriptomic analyses of S. obliquus during mid- and late-log phase growth revealed a dynamic metabolic landscape within many KEGG pathways. Notably, differential expression was observed for several potential glycosyl hydrolases. We also investigated the influence of switchgrass on the growth of S. obliquus at 50 L volume in mini raceway ponds to determine the scalability of this approach.
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Affiliation(s)
- Jenna Y. Schambach
- Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM, United States
| | - Colin P. S. Kruse
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Peter Kitin
- Forest Products Laboratory, Forest Biopolymer Science and Engineering, U.S. Forest Service, Madison, WI, United States
| | - Wittney Mays
- Computational Biology and Biophysics Department, Sandia National Laboratories, Albuquerque, NM, United States
| | - Christopher G. Hunt
- Forest Products Laboratory, Forest Biopolymer Science and Engineering, U.S. Forest Service, Madison, WI, United States
| | - Shawn R. Starkenburg
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Amanda N. Barry
- Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM, United States
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17
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Lawrence G, Midtervoll I, Samuelsen SO, Kristoffersen AK, Enersen M, Håheim LL. The blood microbiome and its association to cardiovascular disease mortality: case-cohort study. BMC Cardiovasc Disord 2022; 22:344. [PMID: 35909117 PMCID: PMC9339179 DOI: 10.1186/s12872-022-02791-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 07/26/2022] [Indexed: 01/29/2023] Open
Abstract
Background Little is known about the association between bacterial DNA in human blood and the risk of cardiovascular disease (CVD) mortality. Methods A case-cohort study was performed based on a 9 ½ year follow-up of the Oslo II study from 2000. Eligible for this analysis were men born in 1923 and from 1926 to 1932. The cases were men (n = 227) who had died from CVD, and the controls were randomly selected participants from the same cohort (n = 178). Analysis of the bacterial microbiome was performed on stored frozen blood samples for both cases and controls. Association analyses for CVD mortality were performed by Cox proportional hazard regression adapted to the case-cohort design. We used the Bonferroni correction due to the many bacterial genera that were identified. Results Bacterial DNA was identified in 372 (82%) of the blood samples and included 78 bacterial genera from six phyla. Three genera were significantly associated with CVD mortality. The genera Kocuria (adjusted hazard ratio (HR) 8.50, 95% confidence interval (CI) (4.05, 17.84)) and Enhydrobacter (HR 3.30 (2.01, 5.57)) indicate an association with CVD mortality with increasing levels. The genera Paracoccus (HR 0.29 (0.15, 0.57)) was inversely related. Significant predictors of CVD mortality were: the feeling of bad health; and the consumption of more than three cups of coffee per day. The following registered factors were borderline significant, namely: a history of heart failure; increased systolic blood pressure; and currently taking antihypertensive drugs now, versus previously. Conclusions The increasing levels of two bacterial genera Kocuria (skin and oral) and Enhydrobacter (skin) and low levels of Paracoccus (soil) were associated with CVD mortality independent of known risk factors for CVD. Supplementary Information The online version contains supplementary material available at 10.1186/s12872-022-02791-7.
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18
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Gupta A, Malwe AS, Srivastava GN, Thoudam P, Hibare K, Sharma VK. MP4: a machine learning based classification tool for prediction and functional annotation of pathogenic proteins from metagenomic and genomic datasets. BMC Bioinformatics 2022; 23:507. [PMID: 36443666 PMCID: PMC9703692 DOI: 10.1186/s12859-022-05061-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 11/16/2022] [Indexed: 11/29/2022] Open
Abstract
Bacteria can exceptionally evolve and develop pathogenic features making it crucial to determine novel pathogenic proteins for specific therapeutic interventions. Therefore, we have developed a machine-learning tool that predicts and functionally classifies pathogenic proteins into their respective pathogenic classes. Through construction of pathogenic proteins database and optimization of ML algorithms, Support Vector Machine was selected for the model construction. The developed SVM classifier yielded an accuracy of 81.72% on the blind-dataset and classified the proteins into three classes: Non-pathogenic proteins (Class-1), Antibiotic Resistance Proteins and Toxins (Class-2), and Secretory System Associated and capsular proteins (Class-3). The classifier provided an accuracy of 79% on real dataset-1, and 72% on real dataset-2. Based on the probability of prediction, users can estimate the pathogenicity and annotation of proteins under scrutiny. Tool will provide accurate prediction of pathogenic proteins in genomic and metagenomic datasets providing leads for experimental validations. Tool is available at: http://metagenomics.iiserb.ac.in/mp4 .
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Affiliation(s)
- Ankit Gupta
- grid.462376.20000 0004 1763 8131MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh India
| | - Aditya S. Malwe
- grid.462376.20000 0004 1763 8131MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh India
| | - Gopal N. Srivastava
- grid.462376.20000 0004 1763 8131MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh India
| | - Parikshit Thoudam
- grid.462376.20000 0004 1763 8131MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh India
| | - Keshav Hibare
- grid.462376.20000 0004 1763 8131MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh India
| | - Vineet K. Sharma
- grid.462376.20000 0004 1763 8131MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh India
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Phylogenetic analysis and characterization of arsenic (As) transforming bacterial marker proteins following isolation of As-tolerant indigenous bacteria. Arch Microbiol 2022; 204:660. [PMID: 36190579 DOI: 10.1007/s00203-022-03270-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/01/2022] [Accepted: 09/22/2022] [Indexed: 11/02/2022]
Abstract
Marker proteins play a significant role in bacterial arsenic (As) transformation. Phylogenetic analysis and three-dimensional (3D) characteristics of As transforming bacterial marker proteins guide the evolutionary origin and As transforming potential of the species. Indeed, As-tolerant bacteria also show a significant level of As transformation. Hence, characterization of As transforming bacterial marker proteins, isolation of As transforming bacteria, and proper integration of the findings may guide to elucidate how bacteria transform As. Therefore, phylogenetic analysis and 3D characterization of As transforming bacterial marker protein following isolation of potential indigenous As-tolerant indigenous bacteria were done to explore the mechanism of bacterial As transformation. Phylogenetic analysis of ten As transforming marker proteins (arsA, arsB, arsC, arsD, arsR, aioA, arrA, aioB, acr1, and acr3) in 20 potential bacterial genomes (except 19 for the acr3) were studied. Some bacterial genomes featured up to five marker proteins, and therefore, 3D characteristics of the marker proteins were analyzed in those genomes having three-to-five marker proteins. In phylogeny, species in close clades represent their phylogenetic resemblances and may have similar functions. P. aeruginosa, E. coli, and K. pneumonia were found to be more effective due to having the highest number (five) of marker proteins. In 3D protein modeling, most of the marker proteins were found to be active. Among 19 indigenous bacterial isolates, multiple isolates showed tolerance up to 50 mM As(III) and 250 mM As(V), which may potentially transform a significant quantities of As. Hence, integration of the results of phylogenetic analysis, 3D protein characteristics, and As tolerance in the bacterial isolates could guide to explore the mechanism of how bacteria transform As at cellular and molecular levels.
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20
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A Wild Rice Rhizobacterium Burkholderia cepacia BRDJ Enhances Nitrogen Use Efficiency in Rice. Int J Mol Sci 2022; 23:ijms231810769. [PMID: 36142689 PMCID: PMC9503923 DOI: 10.3390/ijms231810769] [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: 07/14/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
Rice domestication has dramatically improved its agronomic traits, albeit with unavoidable significantly reduced genetic diversity. Dongxiang common wild rice, the wild rice species distributed in northernmost China, exhibits excellent resistance against stress and diseases and provides a rich genetic resource for rice breeding. Most of the studies focus on the function of the plant genes, often disregarding the role of the root microbes associated with the plants. In this work, we isolated a Burkholderia strain from the root of Dongxiang wild rice, which we identified as Burkholderia cepacia BRDJ, based on a phylogenetic analysis. This strain promoted the rice growth under greenhouse conditions. The grain yield was higher in a rice line containing a small genomic fragment derived from the Dongxiang wild rice, compared to the indica rice cultivar Zhongzao 35. This new strain also increased the plant biomass under limiting nitrogen conditions. Interestingly, this strain had a differential effect on indica and japonica rice varieties under full nitrogen supply conditions. By genome sequencing and comparison with another two B. cepacia strains, we observed enriched genes related with nitrogen fixation and phytohormone and volatiles biosynthesis that may account for the growth-promoting effects of the BRDJ. BRDJ has the potential to be used as a biofertilizer in promoting nitrogen use efficiency and overall growth in rice.
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21
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Assessing the genomic composition, putative ecological relevance and biotechnological potential of plasmids from sponge bacterial symbionts. Microbiol Res 2022; 265:127183. [PMID: 36108440 DOI: 10.1016/j.micres.2022.127183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/24/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022]
Abstract
Plasmid-mediated transfer of genes can have direct consequences in several biological processes within sponge microbial communities. However, very few studies have attempted genomic and functional characterization of plasmids from marine host-associated microbial communities in general and those of sponges in particular. In the present study, we used an endogenous plasmid isolation method to obtain plasmids from bacterial symbionts of the marine sponges Stylissa carteri and Paratetilla sp. and investigated the genomic composition, putative ecological relevance and biotechnological potential of these plasmids. In total, we isolated and characterized three complete plasmids, three plasmid prophages and one incomplete plasmid. Our results highlight the importance of plasmids to transfer relevant genetic traits putatively involved in microbial symbiont adaptation and host-microbe and microbe-microbe interactions. For example, putative genes involved in bacterial response to chemical stress, competition, metabolic versatility and mediation of bacterial colonization and pathogenicity were detected. Genes coding for enzymes and toxins of biotechnological potential were also detected. Most plasmid prophage coding sequences were, however, hypothetical proteins with unknown functions. Overall, this study highlights the ecological relevance of plasmids in the marine sponge microbiome and provides evidence that plasmids of sponge bacterial symbionts may represent an untapped resource of genes of biotechnological interest.
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22
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Hooper MJ, LeWitt TM, Veon FL, Pang Y, Chlipala GE, Feferman L, Green SJ, Sweeney D, Bagnowski KT, Burns MB, Seed PC, Guitart J, Zhou XA. Nasal Dysbiosis in Cutaneous T-Cell Lymphoma Is Characterized by Shifts in Relative Abundances of Non- Staphylococcus Bacteria. JID INNOVATIONS 2022; 2:100132. [PMID: 36161104 PMCID: PMC9500465 DOI: 10.1016/j.xjidi.2022.100132] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 12/26/2022] Open
Abstract
The nasal microbiome of patients with cutaneous T-cell lymphoma (CTCL) remains unexplored despite growing evidence connecting nasal bacteria to skin health and disease. Nasal swabs from 45 patients with CTCL (40 with mycosis fungoides, 5 with Sézary syndrome) and 20 healthy controls from the same geographical region (Chicago Metropolitan Area, Chicago, IL) were analyzed using sequencing of 16S ribosomal RNA and tuf2 gene amplicons. Nasal α-diversity did not differ between mycosis fungoides/Sézary syndrome and healthy controls (Shannon index, genus level, P = 0.201), but distinct microbial communities were identified at the class (R2 = 0.104, P = 0.023) and order (R2 = 0.0904, P = 0.038) levels. Increased relative abundance of the genera Catenococcus, Vibrio, Roseomonas, Acinetobacter, and unclassified Clostridiales was associated with increased skin disease burden (P < 0.005, q < 0.05). Performed to accurately resolve nasal Staphylococcus at the species level, tuf2 gene amplicon sequencing revealed no significant differences between mycosis fungoides/Sézary syndrome and healthy controls. Although S. aureus has been shown to worsen CTCL through its toxins, no increase in the relative abundance of this taxon was observed in nasal samples. Despite the lack of differences in Staphylococcus, the CTCL nasal microbiome was characterized by shifts in numerous other bacterial taxa. These data add to our understanding of the greater CTCL microbiome and provide context for comprehending nasal-skin and host‒tumor‒microbial relationships.
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Affiliation(s)
- Madeline J. Hooper
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Tessa M. LeWitt
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Francesca L. Veon
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Yanzhen Pang
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - George E. Chlipala
- Research Informatics Core, Research Resources Center, University of Illinois Chicago, Chicago, Illinois, USA
| | - Leo Feferman
- Research Informatics Core, Research Resources Center, University of Illinois Chicago, Chicago, Illinois, USA
| | - Stefan J. Green
- Rush Genomics and Microbiome Core Facility, Rush University Medical Center, Chicago, Illinois, USA
| | - Dagmar Sweeney
- Genome Research Core, Genome Research Division, Research Resources Center, University of Illinois Chicago, Chicago, Illinois, USA
| | - Katherine T. Bagnowski
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Michael B. Burns
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Patrick C. Seed
- Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Joan Guitart
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Xiaolong A. Zhou
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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23
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Puri A, Bajaj A, Singh Y, Lal R. Harnessing taxonomically diverse and metabolically versatile genus Paracoccus for bioplastic synthesis and xenobiotic biodegradation. J Appl Microbiol 2022; 132:4208-4224. [PMID: 35294092 DOI: 10.1111/jam.15530] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 03/11/2022] [Accepted: 03/12/2022] [Indexed: 11/26/2022]
Abstract
The genus Paracoccus represents a taxonomically diverse group comprising more than 80 novel species isolated from various pristine and polluted environments. The species are characterized as coccoid shaped Gram-negative bacteria with versatile metabolic attributes and classified as autotrophs, heterotrophs and/or methylotrophs. Present study highlights the up-to-date global taxonomic diversity and critically discusses the significance of genome analysis for identifying the genomic determinants related to functional attributes mainly bioplastic synthesis and biodegradation potential that makes these isolates commercially viable. The analysis accentuates polyphasic and genomic attributes of Paracoccus spp. which could be harnessed for commercial applications and emphasizes the need of integrating genome based computational analysis for evolutionary species and functional diversification. The work reflects on the underexplored genetic potential for bioplastic synthesis which can be harnessed using advanced genomic methods. It also underlines the degradation potential and possible use of naturally-occurring pollutant-degrading Paracoccus isolates for development of biodegradation system and efficient removal of contaminants. The work contemplates plausible use of such potent isolates to establish the plant-microbe interaction, contributing towards contaminated land reclamation. Overall; the work signifies need and application of genome analysis to identify and explore prospective potential of Paracoccus spp. for environmental application towards achieving sustainability.
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Affiliation(s)
- Akshita Puri
- Department of Zoology, University of Delhi, Delhi, India.,Present addresses: P.G.T.D, Zoology, R.T.M Nagpur University, Nagpur, 440033, India
| | - Abhay Bajaj
- Department of Zoology, University of Delhi, Delhi, India.,Present addresses: CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020, India
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, India
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, India.,Present addresses: NASI Senior Scientist Platinum Jubilee Fellow, The Energy and Resources Institute Darbari Seth Block, IHC Complex, Lodhi Road New Delhi-110003, India
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24
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Leinberger J, Holste J, Bunk B, Freese HM, Spröer C, Dlugosch L, Kück AC, Schulz S, Brinkhoff T. High Potential for Secondary Metabolite Production of Paracoccus marcusii CP157, Isolated From the Crustacean Cancer pagurus. Front Microbiol 2021; 12:688754. [PMID: 34262548 PMCID: PMC8273931 DOI: 10.3389/fmicb.2021.688754] [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] [Received: 03/31/2021] [Accepted: 06/03/2021] [Indexed: 11/13/2022] Open
Abstract
Secondary metabolites are key components in microbial ecology by mediating interactions between bacteria and their environment, neighboring species or host organisms. Bioactivities can be beneficial for both interaction partners or provide a competitive advantage only for the producer. Colonizers of confined habitats such as biofilms are known as prolific producers of a great number of bioactive secondary metabolites and are a potential source for novel compounds. We investigated the strain Paracoccus marcusii CP157, which originates from the biofilm on the carapace of a shell disease-affected Cancer pagurus specimen, for its potential to produce bioactive secondary metabolites. Its closed genome contains 22 extrachromosomal elements and several gene clusters potentially involved in biosynthesis of bioactive polyketides, bacteriocins, and non-ribosomal peptides. Culture extracts of CP157 showed antagonistic activities against bacteria from different phyla, but also against microalgae and crustacean larvae. Different HPLC-fractions of CP157 culture extracts had antibacterial properties, indicating that several bioactive compounds are produced by CP157. The bioactive extract contains several small, antibacterial compounds that partially withstand elevated temperatures, extreme pH values and exposure to proteolytic enzymes, providing high stability toward environmental conditions in the natural habitat of CP157. Further, screening of 17 Paracoccus spp. revealed that antimicrobial activity, hemolysis and production of N-acyl homoserine lactones are common features within the genus. Taking into account the large habitat diversity and phylogenetic distance of the tested strains, we hypothesize that bioactive secondary metabolites play a central role in the ecology of Paracoccus spp. in their natural environments.
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Affiliation(s)
- Janina Leinberger
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Jonas Holste
- Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Heike M. Freese
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Leon Dlugosch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Anna-Carlotta Kück
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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25
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Fosso C, Maillart E, Beun B, Touzani F, Mahadeb B, Clevenbergh P. Opportunistic peritonitis in peritoneal dialysis: The example of Paracoccus yeei. Clin Case Rep 2021; 9:e04176. [PMID: 34026181 PMCID: PMC8133084 DOI: 10.1002/ccr3.4176] [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: 12/21/2020] [Revised: 03/08/2021] [Accepted: 03/27/2021] [Indexed: 11/06/2022] Open
Abstract
Paracoccus yeei, a Gram-negative coccobacillus, is an emergent opportunistic pathogen. It originates from soil and water. VITEK and MALDI-TOF are used for identification. There are few reports of peritoneal dialysis peritonitis. Its presentation is usually indolent. It can be successfully treated with several antibiotics: β-lactams, aminoglycosides, without removing the catheter.
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Affiliation(s)
| | | | - Bram Beun
- Laboratoire des Hôpitaux Universitaires de BruxellesBrusselsBelgium
| | - Fahd Touzani
- Nephrology DepartmentCHU BrugmannBrusselsBelgium
| | - Bhavna Mahadeb
- Infectious Diseases DepartmentCHU BrugmannBrusselsBelgium
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26
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Puri A, Bajaj A, Lal S, Singh Y, Lal R. Phylogenomic Framework for Taxonomic Delineation of Paracoccus spp. and Exploration of Core-Pan Genome. Indian J Microbiol 2021; 61:180-194. [PMID: 33927459 DOI: 10.1007/s12088-021-00929-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 02/24/2021] [Indexed: 11/26/2022] Open
Abstract
The taxonomic classification of metabolically versatile Paracoccus spp. has been so far performed using polyphasic approach. The topology of single gene phylogenies, however, has highlighted ambiguous species assignments. In the present study, genome based multi-gene phylogenies and overall genome related index were used for species threshold assessment. Comprehensive phylogenomic analysis of Paracoccus genomes (n = 103) showed concordant clustering of strains across multi-gene marker set phylogenies (nMC = 0.08-0.14); as compared to 16S rDNA phylogeny (nMC = 0.37-0.42) suggesting robustness of multi gene phylogenies in drawing phylogenetic inferences. Functional gene content distribution across the genus showed that only 1.7% gene content constitutes the core genome highlighting the significance of extensive genomic variability in the evolution of Paracoccus spp. Further, genome metrics were used to validate characterized strains, identifying classification anomalies (n = 13), and based on this, genome derived taxonomic amendments were notified in present study. Conclusively, validated metric tools can be employed on whole genome sequences, including draft assemblies, for the assessment and assignment of uncharacterized strains and species level ascription of newly isolated Paracoccus strains in future.
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Affiliation(s)
- Akshita Puri
- Department of Zoology, University of Delhi, Delhi, India
- Present Address: P.G.T.D, Zoology, R.T.M Nagpur University, Nagpur, 440033 India
| | - Abhay Bajaj
- Department of Zoology, University of Delhi, Delhi, India
- Present Address: EBGD, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020 India
| | - Sukanya Lal
- Present Address: Ramjas College, University of Delhi, Delhi, India
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, India
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, India
- Present Address: The Energy and Resources Institute Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003 India
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27
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Chen Z, Erickson DL, Meng J. Polishing the Oxford Nanopore long-read assemblies of bacterial pathogens with Illumina short reads to improve genomic analyses. Genomics 2021; 113:1366-1377. [PMID: 33716184 DOI: 10.1016/j.ygeno.2021.03.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/18/2021] [Accepted: 03/08/2021] [Indexed: 11/18/2022]
Abstract
Oxford Nanopore sequencing has been widely used to achieve complete genomes of bacterial pathogens. However, the error rates of Oxford Nanopore long reads are high. Various polishing algorithms using Illumina short reads to correct the errors in Oxford Nanopore long-read assemblies have been developed. The impact of polishing the Oxford Nanopore long-read assemblies of bacterial pathogens with Illumina short reads on improving genomic analyses was evaluated using both simulated and real reads. Ten species (10 strains) were selected for simulated reads, while real reads were tested on 11 species (11 strains). Oxford Nanopore long reads were assembled with Unicycler to produce a draft assembly, followed by three rounds of polishing with Illumina short reads using two polishing tools, Pilon and NextPolish. One round of NextPolish polishing generated genome completeness and accuracy parameters similar to the reference genomes, whereas two or three rounds of Pilon polishing were needed, though contiguity remained unchanged after polishing. The polished assemblies of Escherichia coli O157:H7, Salmonella Typhimurium, and Cronobacter sakazakii with simulated reads did not provide accurate plasmid identifications. One round of NextPolish polishing was needed for accurately identifying plasmids in Staphylococcus aureus and E. coli O26:H11 with real reads, whereas one and two rounds of Pilon polishing were necessary for these two strains, respectively. Polishing failed to provide an accurate antimicrobial resistance (AMR) genotype for S. aureus with real reads. One round of polishing recovered an accurate AMR genotype for Klebsiella pneumoniae with real reads. The reference genome and draft assembly of Citrobacter braakii with real reads differed, which carried blaCMY-83 and fosA6, respectively, while both genes were present after one round of polishing. However, polishing did not improve the assembly of E. coli O26:H11 with real reads to achieve numbers of virulence genes similar to the reference genome. The draft and polished assemblies showed a phylogenetic tree topology comparable with the reference genomes. For multilocus sequence typing and pan-genome analyses, one round of NextPolish polishing was sufficient to obtain accurate results, while two or three rounds of Pilon polishing were needed. Overall, NextPolish outperformed Pilon for polishing the Oxford Nanopore long-read assemblies of bacterial pathogens, though both polishing strategies improved genomic analyses compared to the draft assemblies.
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Affiliation(s)
- Zhao Chen
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA
| | - David L Erickson
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA; Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA.
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28
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The porcine corneal surface bacterial microbiome: A distinctive niche within the ocular surface. PLoS One 2021; 16:e0247392. [PMID: 33606829 PMCID: PMC7895408 DOI: 10.1371/journal.pone.0247392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 02/05/2021] [Indexed: 02/08/2023] Open
Abstract
Purpose The ocular surface microbiome has been described as paucibacterial. Until now, studies investigating the bacterial community associated with the ocular surface through high-throughput sequencing have focused on the conjunctiva. Conjunctival samples are thought to reflect and be representative of the microbiome residing on the ocular surface, including the cornea. Here, we hypothesized that the bacterial community associated with the corneal surface was different from those of the inferonasal and superotemporal conjunctival fornices, and from the tear film. Methods Both eyes from 15 healthy piglets were sampled using swabs (inferonasal fornix, superotemporal fornix, and corneal surface, n = 30 each) and Schirmer tear test strips (STT, n = 30). Negative sampling controls (swabs and STT, n = 2 each) and extraction controls (n = 4) were included. Total DNA was extracted and high-throughput sequencing targeting the 16S rRNA gene was performed. Bioinformatic analyses included multiple contamination-controlling steps. Results Corneal surface samples had a significantly lower number of taxa detected (P<0.01) and were compositionally different from all other sample types (Bray-Curtis dissimilarity, P<0.04). It also harbored higher levels of Proteobacteria (P<0.05), specifically Brevundimonas spp. (4.1-fold) and Paracoccus spp. (3.4-fold) than other sample types. Negative control STT strip samples yielded the highest amount of 16S rRNA gene copies across all sample types (P<0.05). Conclusions Our data suggests that the corneal surface provides a distinct environmental niche within the ocular surface, leading to a bacterial community compositionally different from all other sample types.
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29
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Longitudinal Study of Viral and Bacterial Contamination of Hospital Pediatricians' Mobile Phones. Microorganisms 2020; 8:microorganisms8122011. [PMID: 33339327 PMCID: PMC7766489 DOI: 10.3390/microorganisms8122011] [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: 11/20/2020] [Revised: 12/10/2020] [Accepted: 12/14/2020] [Indexed: 11/17/2022] Open
Abstract
Mobile phones (MPs) of healthcare workers (HCWs) may represent an important source of transmission of infectious agents. This longitudinal study documents the contamination of these tools. Ten MPs handled by senior pediatricians were sampled once a week during 23 weeks in three pediatric wards of the University Hospital of Saint-Etienne, France. Cultures were performed for bacteria and multiplex PCR assays for a panel of respiratory and enteric viruses. A questionnaire on hygiene habits regarding phoning and care was filled-in by pediatricians before and after the study. From a total of 230 samples, 145 (63%) were contaminated by at least one pathogen. The MPs from emergency departments were the most impacted. Viruses were detected in 179 samples; bacteria were isolated in 59 samples. Contamination increased during the winter epidemic peak. A cross-contamination by Paracoccus yeei between hands and MPs of different HCWs was demonstrated. The communication of the study results influenced the hygiene behaviors. This study highlights the contamination of MPs by pathogens that are resistant in the environment, and its sustainability along the winter season. The role of MPs as vectors of nosocomial infection needs to be better investigated.
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30
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Li M, Xu J, Jiang Z, Li Q. Molecular understanding of autotrophic CO2-fixing bacterial communities in composting based on RuBisCO genes analysis. J Biotechnol 2020; 320:36-43. [DOI: 10.1016/j.jbiotec.2020.06.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 05/31/2020] [Accepted: 06/12/2020] [Indexed: 12/17/2022]
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31
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Fritz B, Schäfer K, März M, Wahl S, Ziemssen F, Egert M. Eye-Catching Microbes-Polyphasic Analysis of the Microbiota on Microscope Oculars Verifies Their Role as Fomites. J Clin Med 2020; 9:jcm9051572. [PMID: 32455878 PMCID: PMC7290821 DOI: 10.3390/jcm9051572] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 11/16/2022] Open
Abstract
Microscopes are used in virtually every biological and medical laboratory. Previous cultivation-based studies have suggested that direct contact with microscope eyepieces increases the risk of eye infections. To obtain a deeper insight into the microbiota on oculars, we analysed 10 recently used university microscopes. Their left oculars were used for a cultivation-based approach, while the right oculars served for massive gene sequencing. After cleaning with isopropyl alcohol, the oculars were re-sampled and analysed again. All oculars were found to be contaminated with bacteria, with a maximum load of 1.7 × 103 CFU cm-2. MALDI Biotyping revealed mainly Cutibacterium (68%), Staphylococcus (14%) and Brevibacterium (10%), with the most abundant species being Cutibacterium acnes (13%) and Staphylococcus capitis (6%). Cleaning reduced the microbial load by up to 2 log scales. Within 10 uncleaned and 5 cleaned samples, 1480 ASVs were assigned to 10 phyla and 262 genera. The dominant genera before cleaning were Cutibacterium (78%), Paracoccus (13%), Pseudomonas (2%) and Acinetobacter (1%). The bacteriota composition on the cleaned oculars was similar; however, it probably largely represented dead bacteria. In summary, used oculars were significantly contaminated with skin and environmental bacteria, including potential pathogens. Regular cleaning is highly recommended to prevent eye and skin infections.
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Affiliation(s)
- Birgit Fritz
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054 Villingen-Schwenningen, Germany; (B.F.); (K.S.); (M.M.)
| | - Karin Schäfer
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054 Villingen-Schwenningen, Germany; (B.F.); (K.S.); (M.M.)
| | - Melanie März
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054 Villingen-Schwenningen, Germany; (B.F.); (K.S.); (M.M.)
| | - Siegfried Wahl
- Carl Zeiss Vision International GmbH, Turnstrasse 27, 73430 Aalen, Germany;
- Institute for Ophthalmic Research, Eberhard-Karls University, Elfriede-Aulhorn-Strasse 7, 72076 Tuebingen, Germany
| | - Focke Ziemssen
- Center for Ophthalmology, Eberhard-Karls University, Elfriede-Aulhorn-Strasse 7, 72076 Tuebingen, Germany;
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054 Villingen-Schwenningen, Germany; (B.F.); (K.S.); (M.M.)
- Correspondence: ; Tel.: +49-7720-307-4554
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Zhou G, Qiu X, Zhang J, Tao C. Effects of seaweed fertilizer on enzyme activities, metabolic characteristics, and bacterial communities during maize straw composting. BIORESOURCE TECHNOLOGY 2019; 286:121375. [PMID: 31030066 DOI: 10.1016/j.biortech.2019.121375] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/19/2019] [Accepted: 04/20/2019] [Indexed: 06/09/2023]
Abstract
The objective of this study was to investigate microbial responses when seaweed fertilizer was added to maize straw compost. The metabolic characteristics and bacterial communities were assessed using 16S rRNA sequencing and Biolog analysis. Results showed that the urease, dehydrogenase, and metabolic activities improved on day 21 after the addition of seaweed fertilizer. Firmicutes, Proteobacteria, and Actinobacteria were the dominant phyla in the compost. The relative abundances of Proteobacteria and Actinobacteria were increased by addition of seaweed fertilizer during the early composting stage. Temperature, NH4+-N, NO3--N concentrations, and carbon source metabolism had close relationships with bacterial community variation during composting. A network analysis revealed that NO3--N content had a positive association with Aeromicrobium, and seaweed fertilizer application improved the growth of keystone species related to N cycling. These results suggested that seaweed fertilizer influenced bacterial community succession through its effects on N concentrations during the composting process.
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Affiliation(s)
- Guixiang Zhou
- Poyang Lake Eco-economy Research Center, Jiujiang University, Jiujiang 332005, China; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiuwen Qiu
- Poyang Lake Eco-economy Research Center, Jiujiang University, Jiujiang 332005, China; Office of Mountain-River-Lake Development Committee of Jiangxi Province, Nanchang 330046, China.
| | - Jiabao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chunyuan Tao
- Poyang Lake Eco-economy Research Center, Jiujiang University, Jiujiang 332005, China
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Decewicz P, Dziewit L, Golec P, Kozlowska P, Bartosik D, Radlinska M. Characterization of the virome of Paracoccus spp. (Alphaproteobacteria) by combined in silico and in vivo approaches. Sci Rep 2019; 9:7899. [PMID: 31133656 PMCID: PMC6536676 DOI: 10.1038/s41598-019-44460-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/17/2019] [Indexed: 12/19/2022] Open
Abstract
Bacteria of the genus Paracoccus inhabit various pristine and anthropologically-shaped environments. Many Paracoccus spp. have biotechnological value and several are opportunistic human pathogens. Despite extensive knowledge of their metabolic potential and genome architecture, little is known about viruses of Paracoccus spp. So far, only three active phages infecting these bacteria have been identified. In this study, 16 Paracoccus strains were screened for the presence of active temperate phages, which resulted in the identification of five novel viruses. Mitomycin C-induced prophages were isolated, visualized and their genomes sequenced and thoroughly analyzed, including functional validation of their toxin-antitoxin systems. This led to the identification of the first active Myoviridae phage in Paracoccus spp. and four novel Siphoviridae phages. In addition, another 53 prophages were distinguished in silico within genomic sequences of Paracoccus spp. available in public databases. Thus, the Paracoccus virome was defined as being composed of 66 (pro)phages. Comparative analyses revealed the diversity and mosaicism of the (pro)phage genomes. Moreover, similarity networking analysis highlighted the uniqueness of Paracoccus (pro)phages among known bacterial viruses.
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Affiliation(s)
- Przemyslaw Decewicz
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Bacterial Genetics, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Lukasz Dziewit
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Bacterial Genetics, Miecznikowa 1, 02-096, Warsaw, Poland.
| | - Piotr Golec
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Bacterial Genetics, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Patrycja Kozlowska
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Virology, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Dariusz Bartosik
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Bacterial Genetics, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Monika Radlinska
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Virology, Miecznikowa 1, 02-096, Warsaw, Poland
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