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Hernández-Melgar AG, Guerrero A, Moreno-Ulloa A. Chronic Exposure to Petroleum-Derived Hydrocarbons Alters Human Skin Microbiome and Metabolome Profiles: A Pilot Study. J Proteome Res 2024; 23:4273-4285. [PMID: 39024464 DOI: 10.1021/acs.jproteome.4c00256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Petroleum-derived substances, like industrial oils and grease, are ubiquitous in our daily lives. Comprised of petroleum hydrocarbons (PH), these substances can come into contact with our skin, potentially causing molecular disruptions and contributing to the development of chronic disease. In this pilot study, we employed mass spectrometry-based untargeted metabolomics and 16S rRNA gene sequencing analyses to explore these effects. Superficial skin samples were collected from subjects with and without chronic dermal exposure to PH at two anatomical sites: the fingers (referred to as the hand) and arms (serving as an intersubject variability control). Exposed hands exhibited higher bacterial diversity (Shannon and Simpson indices) and an enrichment of oil-degrading bacteria (ODB), including Dietzia, Paracoccus, and Kocuria. Functional prediction suggested enriched pathways associated with PH degradation in exposed hands vs non-exposed hands, while no differences were observed when comparing the arms. Furthermore, carboxylic acids, glycerophospholipids, organooxygen compounds, phenol ethers, among others, were found to be more abundant in exposed hands. We observed positive correlations among multiple ODB and xenobiotics, suggesting a chemical remodeling of the skin favorable for ODB thriving. Overall, our study offers insights into the complex dysregulation of bacterial communities and the chemical milieu induced by chronic dermal exposure to PH.
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Affiliation(s)
- Alan G Hernández-Melgar
- MS2 Laboratory, Biomedical Innovation Department, Ensenada Center for Scientific Research and Higher Education, Baja California (CICESE), No. 3918, Zona Playitas, Ensenada 22860, Baja California, Mexico
- Posgrado en Ciencias de la Vida, CICESE, Ensenada 22860, Baja California, Mexico
| | - Abraham Guerrero
- CONAHCyT Research, Research Center in Food & Development A.C. (CIAD), Mazatlán 82112, Sinaloa, Mexico
| | - Aldo Moreno-Ulloa
- MS2 Laboratory, Biomedical Innovation Department, Ensenada Center for Scientific Research and Higher Education, Baja California (CICESE), No. 3918, Zona Playitas, Ensenada 22860, Baja California, Mexico
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Hirsch AM, Khan N, Humm E, Rubbi M, Del Vecchio G, Ha SM, Pellegrini M, Gunsalus RP. Genome of Dietzia cinnamea 55, a desert-isolated microbe with plant growth-promoting properties for grain crops. Microbiol Resour Announc 2024:e0025724. [PMID: 39254331 DOI: 10.1128/mra.00257-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 07/30/2024] [Indexed: 09/11/2024] Open
Abstract
Here, we report the genome sequence of Dietzia cinnamea 55, isolated from the Negev Desert, Israel. D. cinnamea 55 was found to promote the growth of several cereal crops (corn, wheat, and pearl millet) in greenhouse and field studies.
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Affiliation(s)
- Ann M Hirsch
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, USA
| | - Noor Khan
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, USA
| | - Ethan Humm
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA
| | - Mila Rubbi
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, USA
| | - Giorgia Del Vecchio
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, USA
| | - Sung Min Ha
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, USA
- UCLA DOE Institute, University of California, Los Angeles, California, USA
| | - Robert P Gunsalus
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA
- UCLA DOE Institute, University of California, Los Angeles, California, USA
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3
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Bishop SL, Solonenka JT, Giebelhaus RT, Bakker DTR, Li ITS, Murch SJ. Microbial Diversity Impacts Non-Protein Amino Acid Production in Cyanobacterial Bloom Cultures Collected from Lake Winnipeg. Toxins (Basel) 2024; 16:169. [PMID: 38668594 PMCID: PMC11053616 DOI: 10.3390/toxins16040169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/10/2024] [Accepted: 03/20/2024] [Indexed: 04/29/2024] Open
Abstract
Lake Winnipeg in Manitoba, Canada is heavily impacted by harmful algal blooms that contain non-protein amino acids (NPAAs) produced by cyanobacteria: N-(2-aminoethyl)glycine (AEG), β-aminomethyl-L-alanine (BAMA), β-N-methylamino-L-alanine (BMAA), and 2,4-diaminobutyric acid (DAB). Our objective was to investigate the impact of microbial diversity on NPAA production by cyanobacteria using semi-purified crude cyanobacterial cultures established from field samples collected by the Lake Winnipeg Research Consortium between 2016 and 2021. NPAAs were detected and quantified by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) using validated analytical methods, while Shannon and Simpson alpha diversity scores were determined from 16S rRNA metagenomic sequences. Alpha diversity in isolate cultures was significantly decreased compared to crude cyanobacterial cultures (p < 0.001), indicating successful semi-purification. BMAA and AEG concentrations were higher in crude compared to isolate cultures (p < 0.0001), and AEG concentrations were correlated to the alpha diversity in cultures (r = 0.554; p < 0.0001). BAMA concentrations were increased in isolate cultures (p < 0.05), while DAB concentrations were similar in crude and isolate cultures. These results demonstrate that microbial community complexity impacts NPAA production by cyanobacteria and related organisms.
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Affiliation(s)
- Stephanie L. Bishop
- Department of Chemistry, University of British Columbia, Syilx Okanagan Nation Territory, Kelowna, BC V1V 1V7, Canada; (J.T.S.); (R.T.G.); (D.T.R.B.); (I.T.S.L.); (S.J.M.)
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Julia T. Solonenka
- Department of Chemistry, University of British Columbia, Syilx Okanagan Nation Territory, Kelowna, BC V1V 1V7, Canada; (J.T.S.); (R.T.G.); (D.T.R.B.); (I.T.S.L.); (S.J.M.)
| | - Ryland T. Giebelhaus
- Department of Chemistry, University of British Columbia, Syilx Okanagan Nation Territory, Kelowna, BC V1V 1V7, Canada; (J.T.S.); (R.T.G.); (D.T.R.B.); (I.T.S.L.); (S.J.M.)
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2N4, Canada
- The Metabolomics Innovation Centre, Edmonton, AB T6G 2N4, Canada
| | - David T. R. Bakker
- Department of Chemistry, University of British Columbia, Syilx Okanagan Nation Territory, Kelowna, BC V1V 1V7, Canada; (J.T.S.); (R.T.G.); (D.T.R.B.); (I.T.S.L.); (S.J.M.)
| | - Isaac T. S. Li
- Department of Chemistry, University of British Columbia, Syilx Okanagan Nation Territory, Kelowna, BC V1V 1V7, Canada; (J.T.S.); (R.T.G.); (D.T.R.B.); (I.T.S.L.); (S.J.M.)
| | - Susan J. Murch
- Department of Chemistry, University of British Columbia, Syilx Okanagan Nation Territory, Kelowna, BC V1V 1V7, Canada; (J.T.S.); (R.T.G.); (D.T.R.B.); (I.T.S.L.); (S.J.M.)
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Těšický M, Schmiedová L, Krajzingrová T, Samblas MG, Bauerová P, Kreisinger J, Vinkler M. Nearly (?) sterile avian egg in a passerine bird. FEMS Microbiol Ecol 2024; 100:fiad164. [PMID: 38115624 PMCID: PMC10791042 DOI: 10.1093/femsec/fiad164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 12/02/2023] [Accepted: 12/18/2023] [Indexed: 12/21/2023] Open
Abstract
During early ontogeny, microbiome affects development of the gastrointestinal tract, immunity, and survival in vertebrates. Bird eggs are thought to be (1) initially sterile (sterile egg hypothesis) and (2) colonized after oviposition through horizontal trans-shell migration, or (3) initially seeded with bacteria by vertical transfer from mother oviduct. To date, however, little empirical data illuminate the contribution of these mechanisms to gut microbiota formation in avian embryos. We investigated microbiome of the egg content (day 0; E0-egg), embryonic gut at day 13 (E13) and female faeces in a free-living passerine, the great tit (Parus major), using a methodologically advanced procedure combining 16S rRNA gene sequencing and microbe-specific qPCR assays. Our metabarcoding revealed that the avian egg is (nearly) sterile, but acquires a slightly richer microbiome during the embryonic development. Of the three potentially pathogenic bacteria targeted by qPCR, only Dietzia was found in E0-egg (yet also in negative controls), E13 gut and female samples, which might indicate possible vertical transfer. Unlike in poultry, we have shown that major bacterial colonization of the gut in passerines does not occur before hatching. We emphasize that protocols that carefully check for environmental contamination are critical in studies with low-bacterial biomass samples.
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Affiliation(s)
- Martin Těšický
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, 128 43 Prague, Czech Republic
- Institute of Vertebrate Biology, v.v.i., The Czech Academy of Sciences, Květná 8, Brno 603 65, Czech Republic
- Institute of Paleonatomy, Domestification Research and History of Veterinary Medicine, Ludwig Maxmilian University of Munich, Kaulbachstr. 37 III, 80539 Munich, Germany
| | - Lucie Schmiedová
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, 128 43 Prague, Czech Republic
- Institute of Vertebrate Biology, v.v.i., The Czech Academy of Sciences, Květná 8, Brno 603 65, Czech Republic
| | - Tereza Krajzingrová
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, 128 43 Prague, Czech Republic
| | - Mercedes Gomez Samblas
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, 128 43 Prague, Czech Republic
- Faculty of Science, Department of Parasitology, Campus Universitario de Fuentenueva, University of Granada, Profesor Adolfo Rancano, 18071 Granada, Spain
| | - Petra Bauerová
- Division of Air Quality, Czech Hydrometeorological Institute
, Tušimice Observatory, Tušimice 6, 432 01 Kadaň, Czech Republic
| | - Jakub Kreisinger
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, 128 43 Prague, Czech Republic
| | - Michal Vinkler
- Faculty of Science, Department of Zoology, Charles University, Viničná 7, 128 43 Prague, Czech Republic
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Zhang YD, Fan SJ, Zhang Z, Li JX, Liu XX, Hu LX, Knibbs LD, Dadvand P, Jalaludin B, Browning MH, Zhao T, Heinrich J, He Z, Chen CZ, Zhou Y, Dong GH, Yang BY. Association between Residential Greenness and Human Microbiota: Evidence from Multiple Countries. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:87010. [PMID: 37585351 PMCID: PMC10431502 DOI: 10.1289/ehp12186] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 07/06/2023] [Accepted: 07/17/2023] [Indexed: 08/18/2023]
Abstract
BACKGROUND Greenness, referring to a measurement of the density of vegetated land (e.g., gardens, parks, grasslands), has been linked with many human health outcomes. However, the evidence on greenness exposure and human microbiota remains limited, inconclusive, drawn from specific regions, and based on only modest sample size. OBJECTIVES We aimed to study the association between greenness exposure and human microbial diversity and composition in a large sample across 34 countries and regions. METHODS We explored associations between residential greenness and human microbial alpha-diversity, composition, and genus abundance using data from 34 countries. Greenness exposure was assessed using the normalized difference vegetation index and the enhanced vegetation index mean values in the month before sampling. We used linear regression models to estimate the association between greenness and microbial alpha-diversity and tested the effect modification of age, sex, climate zone, and pet ownership of participants. Differences in microbial composition were tested by permutational multivariate analysis of variance based on Bray-Curtis distance and differential taxa were detected using the DESeq2 R package between two greenness exposure groups split by median values of greenness. RESULTS We found that higher greenness was significantly associated with greater richness levels in the palm and gut microbiota but decreased evenness in the gut microbiota. Pet ownership and climate zone modified some associations between greenness and alpha-diversity. Palm and gut microbial composition at the genus level also varied by greenness. Higher abundances of the genera Lactobacillus and Bifidobacterium, and lower abundances of the genera Anaerotruncus and Streptococcus, were observed in people with higher greenness levels. DISCUSSION These findings suggest that residential greenness was associated with microbial richness and composition in the human skin and gut samples, collected across different geographic contexts. Future studies may validate the observed associations and determine whether they correspond to improvements in human health. https://doi.org/10.1289/EHP12186.
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Affiliation(s)
- Yi-Dan Zhang
- Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Shu-Jun Fan
- Department of Environmental Health, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
- Institute of Public Health, Guangzhou Medical University and Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Zheng Zhang
- Department of Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Jia-Xin Li
- Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Xiao-Xuan Liu
- Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Li-Xin Hu
- Department of Maternal and Child Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Luke D. Knibbs
- School of Public Health, University of Sydney, Camperdown, New South Wales, Australia
| | - Payam Dadvand
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Bin Jalaludin
- School of Population Health, University of New South Wales, Kensington, New South Wales, Australia
| | - Matthew H.E.M. Browning
- Department of Park, Recreation, and Tourism Management, Clemson University, Clemson, South Carolina, USA
| | - Tianyu Zhao
- Institute and Clinic for Occupational, Social and Environmental Medicine, Hospital of the Ludwig-Maximilians-Universität München (LMU Munich), Munich, Germany
- Comprehensive Pneumology Center Munich, LMU Munich, Munich, Germany
- German Center for Lung Research, Justus Liebig University Giessen, Giessen, Germany
- Institute of Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
| | - Joachim Heinrich
- Institute and Clinic for Occupational, Social and Environmental Medicine, LMU Munich, Munich, Germany
- Allergy and Lung Health Unit, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Zhini He
- Food Safety and Health Research Center, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Cheng-Zhi Chen
- School of Public Health and Management, Research Center for Medicine and Social Development, Innovation Center for Social Risk Governance in Health, Chongqing Medical University, Chongqing, China
| | - Yuanzhong Zhou
- Department of Epidemiology, School of Public Health, Zunyi Medical University, Zunyi, China
| | - Guang-Hui Dong
- Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Bo-Yi Yang
- Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
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Santos RGD, Hurtado R, Rodrigues DLN, Lima A, Dos Anjos WF, Rifici C, Attili AR, Tiwari S, Jaiswal AK, Spier SJ, Mazzullo G, Morais-Rodrigues F, Gomide ACP, de Jesus LCL, Aburjaile FF, Brenig B, Cuteri V, Castro TLDP, Seyffert N, Santos A, Góes-Neto A, de Jesus Sousa T, Azevedo V. Comparative genomic analysis of the Dietzia genus: an insight into genomic diversity, and adaptation. Res Microbiol 2023; 174:103998. [PMID: 36375718 DOI: 10.1016/j.resmic.2022.103998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/27/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
Dietzia strains are widely distributed in the environment, presenting an opportunistic role, and some species have undetermined taxonomic characteristics. Here, we propose the existence of errors in the classification of species in this genus using comparative genomics. We performed ANI, dDDH, pangenome and genomic plasticity analyses better to elucidate the phylogenomic relationships between Dietzia strains. For this, we used 55 genomes of Dietzia downloaded from public databases that were combined with a newly sequenced. Sequence analysis of a phylogenetic tree based on genome similarity comparisons and dDDH, ANI analyses supported grouping different Dietzia species into four distinct groups. The pangenome analysis corroborated the classification of these groups, supporting the idea that some species of Dietzia could be reassigned in a possible classification into three distinct species, each containing less variability than that found within the global pangenome of all strains. Additionally, analysis of genomic plasticity based on groups containing Dietzia strains found differences in the presence and absence of symbiotic Islands and pathogenic islands related to their isolation site. We propose that the comparison of pangenome subsets together with phylogenomic approaches can be used as an alternative for the classification and differentiation of new species of the genus Dietzia.
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Affiliation(s)
- Roselane Gonçalves Dos Santos
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Raquel Hurtado
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Diego Lucas Neres Rodrigues
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Alessandra Lima
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Claudia Rifici
- Department of Veterinary Science, University of Messina (Italy), Polo Universitario dell'Annunziata, 98168 Messina (ME), Italy.
| | - Anna Rita Attili
- School of Biosciences and Veterinary Medicine, University of Camerino (Italy), Via Circonvallazione 93/95, 62024 Matelica (MC), Italy.
| | - Sandeep Tiwari
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil; Postgraduate Program in Microbiology, Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil; Postgraduate Program in Immunology, Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | - Arun Kumar Jaiswal
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sharon J Spier
- Department of Veterinary Medicine and Epidemiology, University of California, Davis, CA, USA.
| | - Giuseppe Mazzullo
- Department of Veterinary Science, University of Messina (Italy), Polo Universitario dell'Annunziata, 98168 Messina (ME), Italy.
| | - Francielly Morais-Rodrigues
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Anne Cybelle Pinto Gomide
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Luís Cláudio Lima de Jesus
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Flavia Figueira Aburjaile
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, Göttingen, Germany.
| | - Vincenzo Cuteri
- School of Biosciences and Veterinary Medicine, University of Camerino (Italy), Via Circonvallazione 93/95, 62024 Matelica (MC), Italy.
| | - Thiago Luiz de Paula Castro
- Postgraduate Program in Microbiology, Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil; Postgraduate Program in Immunology, Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil; Department of Biotechnology, Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil.
| | - Núbia Seyffert
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil; Postgraduate Program in Microbiology, Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil.
| | - Anderson Santos
- Department of Computer Science, Federal University of Uberlandia, Uberlandia, Brazil
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais Brazil.
| | - Thiago de Jesus Sousa
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Vasco Azevedo
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
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Reiss Z, Rob F, Kolar M, Schierova D, Kreisinger J, Jackova Z, Roubalova R, Coufal S, Mihula M, Thon T, Bajer L, Novakova M, Vasatko M, Kostovcikova K, Galanova N, Lukas M, Kverka M, Tresnak Hercogova J, Tlaskalova-Hogenova H, Jiraskova Zakostelska Z. Skin microbiota signature distinguishes IBD patients and reflects skin adverse events during anti-TNF therapy. Front Cell Infect Microbiol 2023; 12:1064537. [PMID: 36704107 PMCID: PMC9872723 DOI: 10.3389/fcimb.2022.1064537] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/01/2022] [Indexed: 01/11/2023] Open
Abstract
Crohn's disease (CD) and ulcerative colitis (UC) are two forms of inflammatory bowel disease (IBD), where the role of gut but not skin dysbiosis is well recognized. Inhibitors of TNF have been successful in IBD treatment, but up to a quarter of patients suffer from unpredictable skin adverse events (SkAE). For this purpose, we analyzed temporal dynamics of skin microbiota and serum markers of inflammation and epithelial barrier integrity during anti-TNF therapy and SkAE manifestation in IBD patients. We observed that the skin microbiota signature of IBD patients differs markedly from healthy subjects. In particular, the skin microbiota of CD patients differs significantly from that of UC patients and healthy subjects, mainly in the retroauricular crease. In addition, we showed that anti-TNF-related SkAE are associated with specific shifts in skin microbiota profile and with a decrease in serum levels of L-FABP and I-FABP in IBD patients. For the first time, we showed that shifts in microbial composition in IBD patients are not limited to the gut and that skin microbiota and serum markers of the epithelium barrier may be suitable markers of SkAE during anti-TNF therapy.
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Affiliation(s)
- Zuzana Reiss
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Filip Rob
- Department of Dermatovenerology, Second Faculty of Medicine, Charles University, University Hospital Bulovka, Prague, Czechia
| | - Martin Kolar
- IBD Clinical and Research Centre ISCARE a.s., Prague, Czechia
| | - Dagmar Schierova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Zuzana Jackova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Radka Roubalova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Stepan Coufal
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Martin Mihula
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Tomas Thon
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Lukas Bajer
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia,Department of Gastroenterology and Hepatology, Institute of Clinical and Experimental Medicine, Prague, Czechia
| | - Michaela Novakova
- Department of Dermatovenerology, Second Faculty of Medicine, Charles University, University Hospital Bulovka, Prague, Czechia
| | - Martin Vasatko
- IBD Clinical and Research Centre ISCARE a.s., Prague, Czechia
| | - Klara Kostovcikova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Natalie Galanova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Milan Lukas
- IBD Clinical and Research Centre ISCARE a.s., Prague, Czechia,Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University, Prague, Czechia
| | - Miloslav Kverka
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Jana Tresnak Hercogova
- Department of Dermatovenerology, Second Faculty of Medicine, Charles University, University Hospital Bulovka, Prague, Czechia,Prof. Hercogova Dermatology, Prague, Czechia
| | | | - Zuzana Jiraskova Zakostelska
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia,*Correspondence: Zuzana Jiraskova Zakostelska,
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8
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Plant Growth-Promoting Attributes of Zinc Solubilizing Dietzia maris Isolated from Polyhouse Rhizospheric Soil of Punjab. Curr Microbiol 2023; 80:48. [DOI: 10.1007/s00284-022-03147-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
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9
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Lin H, Wu H, Liu F, Yang H, Shen L, Chen J, Zhang X, Zhong Y, Zhang H, Liu Z. Assessing the hepatotoxicity of PFOA, PFOS, and 6:2 Cl-PFESA in black-spotted frogs (Rana nigromaculata) and elucidating potential association with gut microbiota. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 312:120029. [PMID: 36030957 DOI: 10.1016/j.envpol.2022.120029] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Pollution caused by per- and polyfluoroalkyl substances (PFASs) has become a major global concern. The association between PFAS-induced hepatotoxicity and gut microbiota in amphibians, particularly at environmentally relevant concentrations, remains elusive. Herein we exposed male black-spotted frogs (Rana nigromaculata) to 1 and 10 μg/L waterborne perfluorooctanoic acid (PFOA), perfluorooctanesulfonic acid (PFOS), and 6:2 chlorinated polyfluorinated ether sulfonate (6:2 Cl-PFESA) for 21 days; subsequently, liver histopathological, oxidative stress, molecular docking, gene/protein expression, and gut microbiome analyses were conducted. PFOS and 6:2 Cl-PFESA exposure enhanced serum alanine aminotransferase and aspartate aminotransferase activities, and markedly increased hepatic area of vacuoles and inflammatory cell infiltration, while PFOA exposure increased serum alanine aminotransferase but not aspartate aminotransferase activities and affected hepatic area of vacuoles and inflammatory cell infiltration to a lesser extent. All three PFASs elevated catalase, glutathione S-transferase, and glutathione peroxidase activities and glutathione and malondialdehyde contents in the liver, suggesting the induction of oxidative stress. Further, PFASs could bind to mitogen-activated protein kinases (p38, ERK, and JNK), upregulating not only their expression but also the expression of downstream oxidative stress-related genes and that of P-p38, P-ERK, and Nrf2 proteins. In addition, PFAS exposure significantly increased the relative abundance of Proteobacteria and Delftia and decreased that of Firmicutes and Dietzia, Mycoplasma, and Methylobacterium-Methylorubrum in the order of PFOS ≈ 6:2 Cl-PFESA > PFOA. Altogether, it appears that PFOS and 6:2 Cl-PFESA are more toxic than PFOA. Finally, microbiota function prediction, microbiota co-occurrence network, and correlation analysis between gut microbiota and liver indices suggested that PFAS-induced hepatotoxicity was associated with gut microbiota dysbiosis. Our data provide new insights into the role of gut microbiota in PFAS-induced hepatotoxicity in frogs.
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Affiliation(s)
- Huikang Lin
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Haoying Wu
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Fangyi Liu
- Zhejiang Qiushi Environmental Monitoring Co., Ltd, Hangzhou, 310018, China
| | - Hongmei Yang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Lilai Shen
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Jiahuan Chen
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Xiaofang Zhang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China; School of Engineering, Hangzhou Normal University, Hangzhou, 310018, China
| | - Yuchi Zhong
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China; School of Engineering, Hangzhou Normal University, Hangzhou, 310018, China
| | - Hangjun Zhang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China; School of Engineering, Hangzhou Normal University, Hangzhou, 310018, China
| | - Zhiquan Liu
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China; School of Engineering, Hangzhou Normal University, Hangzhou, 310018, China.
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10
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The Bacterial MtrAB Two-Component System Regulates the Cell Wall Homeostasis Responding to Environmental Alkaline Stress. Microbiol Spectr 2022; 10:e0231122. [PMID: 36073914 PMCID: PMC9602371 DOI: 10.1128/spectrum.02311-22] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Throughout the course of evolution, bacteria have developed signal transduction tools such as two-component systems (TCSs) to meet their demands to thrive even under the most challenging environmental conditions. One TCS called MtrAB is commonly found in Actinobacteria and is implicated in cell wall metabolism, osmoprotection, cell proliferation, antigen secretion, and biosynthesis of secondary metabolites. However, precisely how the MtrAB TCS regulates the bacterial responses to external environments remains unclear. Here, we report that the MtrAB TCS regulates the cell envelope response of alkali-tolerant bacterium Dietzia sp. strain DQ12-45-1b to extreme alkaline stimuli. We found that under alkaline conditions, an mtrAB mutant exhibited both reduced growth and abnormal morphology compared to the wild-type strain. Electrophoretic mobility shift assay analysis showed that MtrA binds the promoter of the mraZ gene critical for cell wall homeostasis, suggesting that MtrA directly controls transcription of this regulator. In conclusion, our findings demonstrate that MtrAB TCS is involved in controlling the bacterial response to alkaline stimuli by regulating the expression of the cell wall homeostasis regulator MraZ in Dietzia sp. DQ12-45-1b, providing novel details critical for a mechanistic understanding of how cell wall homeostasis is controlled. IMPORTANCE Microorganisms can be found in most extreme environments, and they have to adapt to a wide range of environmental stresses. The two-component systems (TCSs) found in bacteria detect environmental stimuli and regulate physiological pathways for survival. The MtrAB TCS conserved in Corynebacterineae is critical for maintaining the metabolism of the cell wall components that protects bacteria from diverse environmental stresses. However, how the MtrAB TCS regulates cell wall homeostasis and adaptation under stress conditions is unclear. Here, we report that the MtrAB TCS in Dietzia sp. DQ12-45-1b plays a critical role in alkaline resistance by modulating the cell wall homeostasis through the MtrAB-MraZ pathway. Thus, our work provides a novel regulatory pathway used by bacteria for adaptation and survival under extreme alkaline stresses.
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11
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The Roles of the Two-Component System, MtrAB, in Response to Diverse Cell Envelope Stresses in Dietzia sp. DQ12-45-1b. Appl Environ Microbiol 2022; 88:e0133722. [PMID: 36190258 PMCID: PMC9599347 DOI: 10.1128/aem.01337-22] [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] [Indexed: 11/30/2022] Open
Abstract
Two-component systems (TCSs) act as common regulatory systems allowing bacteria to detect and respond to multiple environmental stimuli, including cell envelope stress. The MtrAB TCS of Actinobacteria is critical for cell wall homeostasis, cell proliferation, osmoprotection, and antibiotic resistance, and thus is found to be highly conserved across this phylum. However, how precisely the MtrAB TCS regulates cellular homeostasis in response to environmental stress remains unclear. Here, we show that the MtrAB TCS plays an important role in the tolerance to different types of cell envelope stresses, including environmental stresses (i.e., oxidative stress, lysozyme, SDS, osmotic pressure, and alkaline pH stresses) and envelope-targeting antibiotics (i.e., isoniazid, ethambutol, glycopeptide, and β-lactam antibiotics) in Dietzia sp. DQ12-45-1b. An mtrAB mutant strain exhibited slower growth compared to the wild-type strain and was characterized by abnormal cell shapes when exposed to various environmental stresses. Moreover, deletion of mtrAB resulted in decreased resistance to isoniazid, ethambutol, and β-lactam antibiotics. Further, Cleavage under targets and tagmentation sequencing (CUT&Tag-seq) and electrophoretic mobility shift assays (EMSAs) revealed that MtrA binds the promoters of genes involved in peptidoglycan biosynthesis (ldtB, ldtA, murJ), hydrolysis (GJR88_03483, GJR88_4713), and cell division (ftsE). Together, our findings demonstrated that the MtrAB TCS is essential for the survival of Dietzia sp. DQ12-45-1b under various cell envelope stresses, primarily by controlling multiple downstream cellular pathways. Our work suggests that TCSs act as global sensors and regulators in maintaining cellular homeostasis, such as during episodes of various environmental stresses. The present study should shed light on the understanding of mechanisms for bacterial adaptivity to extreme environments. IMPORTANCE The multilayered cell envelope is the first line of bacterial defense against various extreme environments. Bacteria utilize a large number of sensing and regulatory systems to maintain cell envelope homeostasis under multiple stress conditions. The two-component system (TCS) is the main sensing and responding apparatus for environmental adaptation. The MtrAB TCS highly conserved in Actinobacteria is critical for cell wall homeostasis, cell proliferation, osmoprotection, and antibiotic resistance. However, how MtrAB works with regard to signals impacting changes to the cell envelope is not fully understood. Here, we found that in the Actinobacterium Dietzia sp. DQ12-45-1b, a TCS named MtrAB is pivotal for ensuring normal cell growth as well as maintaining proper cell morphology in response to various cell envelope stresses, namely, by regulating the expression of cell envelope-related genes. Our findings should greatly advance our understanding of the adaptive mechanisms responsible for maintaining cell integrity in times of sustained environmental shocks.
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12
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Modulatory effect of Gracilaria gracilis on European seabass gut microbiota community and its functionality. Sci Rep 2022; 12:14836. [PMID: 36050345 PMCID: PMC9437047 DOI: 10.1038/s41598-022-17891-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/02/2022] [Indexed: 12/02/2022] Open
Abstract
Seaweeds are an important source of nutrients and bioactive compounds and have a high potential as health boosters in aquaculture. This study evaluated the effect of dietary inclusion of Gracilaria gracilis biomass or its extract on the European seabass (Dicentrarchus labrax) gut microbial community. Juvenile fish were fed a commercial-like diet with 2.5% or 5% seaweed biomass or 0.35% seaweed extract for 47 days. The gut microbiome was assessed by 16S rRNA amplicon sequencing, and its diversity was not altered by the seaweed supplementation. However, a reduction in Proteobacteria abundance was observed. Random forest analysis highlighted the genera Photobacterium, Staphylococcus, Acinetobacter, Micrococcus and Sphingomonas, and their abundances were reduced when fish were fed diets with algae. SparCC correlation network analysis suggested several mutualistic and other antagonistic relationships that could be related to the predicted altered functions. These pathways were mainly related to the metabolism and biosynthesis of protective compounds such as ectoine and were upregulated in fish fed diets supplemented with algae. This study shows the beneficial potential of Gracilaria as a functional ingredient through the modulation of the complex microbial network towards fish health improvement.
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13
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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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14
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Crippen TL, Singh B, Anderson RC, Sheffield CL. Management Practices Affecting Lesser Mealworm Larvae (Alphitobius diaperinus) Associated Microbial Community in a Broiler House and After Relocating With the Litter Into Pastureland. Front Microbiol 2022; 13:875930. [PMID: 35847098 PMCID: PMC9283091 DOI: 10.3389/fmicb.2022.875930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Lesser mealworms are often found infesting production houses used to raise broiler chickens. Previous studies have investigated pathogenic microorganisms associated with the larvae, but a more thorough study relating total microbiome changes due to management procedures and flock rotations was needed. Additionally, there is a question of what microbiota are transferred into the environment when the litter, in which larvae reside, is piled in pastureland for use as fertilizer and where interactions with the soil and other fauna can occur. This study chronicled, by the 16S rRNA sequencing, the bacterial community profile of larvae in a broiler grow-out house synchronizing to when birds were added to and removed from the house over 2.5 years. The profile was found to be relatively constant despite 11 flock rotations and management disruptions, specifically litter cleanout procedures and the addition of new birds or bedding. In contrast, once removed from the controlled broiler house environment and placed into open pastureland, the substantial microbial diversity brought with the larvae showed greater fluctuation in structure with environmental conditions, one of which was rainfall. Surprisingly, these larvae survived at least 19 weeks, so the potential for moving larval-associated microbes into the environment needs further assessment to minimize the risk of relocating foodborne pathogens and also to assess those bacteria-generating metabolites that have benefits to plant growth when using the litter as a fertilizer. The characterization of their microbiome is the first step to investigating the influences of their microbes on the manmade and environmental ecosystems.
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Affiliation(s)
- Tawni L. Crippen
- Southern Plains Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, College Station, TX, United States
- *Correspondence: Tawni L. Crippen,
| | - Baneshwar Singh
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Robin C. Anderson
- Southern Plains Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, College Station, TX, United States
| | - Cynthia L. Sheffield
- Southern Plains Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, College Station, TX, United States
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15
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Zhou Z, Tang L, Yan L, Jia H, Xiong Y, Shang J, Shao C, Zhang Q, Wang H, He L, Hu D, Zhang D. Wild and Captive Environments Drive the Convergence of Gut Microbiota and Impact Health in Threatened Equids. Front Microbiol 2022; 13:832410. [PMID: 35814657 PMCID: PMC9259803 DOI: 10.3389/fmicb.2022.832410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
To explore how the living environment influences the establishment of gut microbiota in different species, as well as the extent to which changes in the living environment caused by captive breeding affect wildlife’s gut microbiota and health, we used 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing to compare the gut microbiome of two species of threatened equids, the Przewalski’s Horse and the Asian wild ass, in the wild and captivity. The results revealed that different species of Equidae living in the same environment showed remarkable convergence of gut microflora. At the same time, captive populations exhibited significantly “unhealthy” microbiota, such as low Alpha diversity, high levels of potentially pathogenic bacteria and biomarkers of physical or psychological disease, and enrichment of microbial functions associated with exogenous exposure and susceptibility, implying that the artificial environment created by captivity may adversely impact the health of wildlife to some extent. Our findings demonstrate the importance of the environmental factors for the establishment of gut microbiota and host health and provide new insights into the conservation of wildlife in captivity from the perspective of the microbiome.
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Affiliation(s)
- Zhichao Zhou
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Liping Tang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Liping Yan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Huiping Jia
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yu Xiong
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jin Shang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | | | - Qiangwei Zhang
- Gansu Endangered Animals Protection Center, Wuwei, China
| | - Hongjun Wang
- Gansu Endangered Animals Protection Center, Wuwei, China
| | - Lun He
- China Wildlife Conservation Association, Beijing, China
| | - Defu Hu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Dong Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- *Correspondence: Dong Zhang, ;
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16
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Møller SA, Rasmussen PU, Frederiksen MW, Madsen AM. Work clothes as a vector for microorganisms: Accumulation, transport, and resuspension of microorganisms as demonstrated for waste collection workers. ENVIRONMENT INTERNATIONAL 2022; 161:107112. [PMID: 35091375 DOI: 10.1016/j.envint.2022.107112] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/18/2022] [Accepted: 01/21/2022] [Indexed: 05/04/2023]
Abstract
Work clothes may act as a vector for the transport of microorganisms leading to second-hand exposure; however, this has not been studied in work environments. We investigated whether microorganisms accumulate on workers' clothes in environments with elevated microbial exposures, and whether they are transported with the clothes and subsequently resuspended to the air. To study this, we selected waste collection workers and potential transport of bacteria and fungi to waste truck cabs via clothes, and compared the microbial communities within truck cabs, in waste collection workers' personal exposure, and on clean T-shirts worn by the workers. Microbial communities were also investigated for the presence of potentially harmful microorganisms. Results showed that microorganisms accumulated in large quantities (GM = 3.69 × 105 CFU/m2/h for bacteria, GM = 8.29 × 104 CFU/m2/h for fungi) on workers' clothes. The concentrations and species composition of airborne fungi in the truck cabs correlated significantly with the accumulation and composition of fungi on clothes and correlated to concentrations (a trend) and species composition of their personal exposures. The same patterns were not found for bacteria, indicating that work clothes to a lesser degree act as a vector for bacteria under waste collection workers' working conditions compared to fungi. Several pathogenic or allergenic microorganisms were present, e.g.: Klebsiella oxytoca, K. pneumoniae, Proteus mirabilis, Providencia rettgeri, Pseudomonas aeruginosa, and Aspergillus fumigatus, A. glaucus, A. nidulans, A. niger, and various Penicillium species. The potential 'take-home' exposure to these microorganisms are of most concern for immunocompromised or atopic individuals or people with open wounds or cuts. In conclusion, the large accumulation of microorganisms on workers' clothes combined with the overlap between fungal species for the different sample types, and the presence of pathogenic and allergenic microorganisms forms the basis for encouragement of good clothing hygiene during and post working hours.
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Affiliation(s)
- Signe Agnete Møller
- The National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100 Copenhagen Ø, Denmark
| | - Pil Uthaug Rasmussen
- The National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100 Copenhagen Ø, Denmark
| | - Margit W Frederiksen
- The National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100 Copenhagen Ø, Denmark
| | - Anne Mette Madsen
- The National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100 Copenhagen Ø, Denmark.
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17
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Brown WD, Feinberg N, Stedman E, Dejace J, Hale AJ. Dietzia cinnamea: An increasingly recognized human pathogen. IDCases 2022; 29:e01539. [PMID: 35756699 PMCID: PMC9218238 DOI: 10.1016/j.idcr.2022.e01539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- William D. Brown
- Larner College of Medicine at the University of Vermont, Burlington, VT, USA
| | - Nina Feinberg
- Larner College of Medicine at the University of Vermont, Burlington, VT, USA
| | | | - Jean Dejace
- Larner College of Medicine at the University of Vermont, Burlington, VT, USA
- University of Vermont Medical Center, Burlington, VT, USA
| | - Andrew J. Hale
- Larner College of Medicine at the University of Vermont, Burlington, VT, USA
- University of Vermont Medical Center, Burlington, VT, USA
- Correspondence to: University of Vermont Medical Center, Infectious Disease Unit, 111 Colchester Avenue, Mailstop 115 SM2, Burlington, VT 05401, USA.
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18
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Identification and antimicrobial susceptibility of Streptomyces and other unusual Actinobacteria clinical isolates in Spain. New Microbes New Infect 2021; 44:100946. [PMID: 34917388 PMCID: PMC8669300 DOI: 10.1016/j.nmni.2021.100946] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 09/22/2021] [Accepted: 11/15/2021] [Indexed: 11/22/2022] Open
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19
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Ramos-Nino ME, Fitzpatrick DM, Eckstrom KM, Tighe S, Dragon JA, Cheetham S. The Kidney-Associated Microbiome of Wild-Caught Artibeus spp. in Grenada, West Indies. Animals (Basel) 2021; 11:ani11061571. [PMID: 34072244 PMCID: PMC8227013 DOI: 10.3390/ani11061571] [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: 04/27/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 12/25/2022] Open
Abstract
Simple Summary Bats are increasingly being recognized as important integrants of zoonotic disease cycles. Studying bat microbiomes could potentially contribute to the epidemiology of emerging infectious diseases in humans. Furthermore, studying the bat’s microbiome gives us the opportunity to look at the microbiome evolution in mammals. Bat microbiome studies have focused mainly on the gut microbiome, but little is known of the microbiome of the kidney, another potential source of disease transmission. Furthermore, many studies on microbiome found in the literature are based on captive animals, which usually alters the natural microbiome. Here, we analyzed kidney samples of wild-caught Artibeus spp., a fructivorous bat species from Grenada, West Indies, using metagenomics. Abstract Bats are capable of asymptomatically carrying a diverse number of microorganisms, including human pathogens, due to their unique immune system. Because of the close contact between bats and humans, there is a possibility for interspecies transmission and consequential disease outbreaks. Herein, high-throughput sequencing was used to determine the kidney-associated microbiome of a bat species abundant in Grenada, West Indies, Artibeus spp. Results indicate that the kidney of these bats can carry potential human pathogens. An endogenous retrovirus, Desmodus rotundus endogenous retrovirus isolate 824, phylogenetically related to betaretroviruses from rodents and New World primates, was also identified.
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Affiliation(s)
- Maria E. Ramos-Nino
- Department of Microbiology, Immunology, and Pharmacology, School of Medicine, St. George’s University, West Indies, Grenada
- Correspondence: ; Tel.: +1-802-8936358
| | - Daniel M. Fitzpatrick
- Department of Pathobiology, School of Veterinary Medicine, St. George’s University, West Indies, Grenada; (D.M.F.); (S.C.)
| | - Korin M. Eckstrom
- Larner School of Medicine, University of Vermont Massively Parallel Sequencing Facility, Burlington, VT 05401, USA; (K.M.E.); (S.T.); (J.A.D.)
| | - Scott Tighe
- Larner School of Medicine, University of Vermont Massively Parallel Sequencing Facility, Burlington, VT 05401, USA; (K.M.E.); (S.T.); (J.A.D.)
| | - Julie A. Dragon
- Larner School of Medicine, University of Vermont Massively Parallel Sequencing Facility, Burlington, VT 05401, USA; (K.M.E.); (S.T.); (J.A.D.)
| | - Sonia Cheetham
- Department of Pathobiology, School of Veterinary Medicine, St. George’s University, West Indies, Grenada; (D.M.F.); (S.C.)
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20
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Arcos SC, Lira F, Robertson L, González MR, Carballeda-Sangiao N, Sánchez-Alonso I, Zamorano L, Careche M, Jiménez-Ruíz Y, Ramos R, Llorens C, González-Muñoz M, Oliver A, Martínez JL, Navas A. Metagenomics Analysis Reveals an Extraordinary Inner Bacterial Diversity in Anisakids (Nematoda: Anisakidae) L3 Larvae. Microorganisms 2021; 9:1088. [PMID: 34069371 PMCID: PMC8158776 DOI: 10.3390/microorganisms9051088] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 11/28/2022] Open
Abstract
L3 larvae of anisakid nematodes are an important problem for the fisheries industry and pose a potential risk for human health by acting as infectious agents causing allergies and as potential vectors of pathogens and microrganisms. In spite of the close bacteria-nematode relationship very little is known of the anisakids microbiota. Fresh fish could be contaminated by bacteria vectored in the cuticle or in the intestine of anisakids when the L3 larvae migrate through the muscles. As a consequence, the bacterial inoculum will be spread, with potential effects on the quality of the fish, and possible clinical effects cannot be discarded. A total of 2,689,113 16S rRNA gene sequences from a total of 113 L3 individuals obtained from fish captured along the FAO 27 fishing area were studied. Bacteria were taxonomically characterized through 1803 representative operational taxonomic units (OTUs) sequences. Fourteen phyla, 31 classes, 52 orders, 129 families and 187 genera were unambiguously identified. We have found as part of microbiome an average of 123 OTUs per L3 individual. Diversity indices (Shannon and Simpson) indicate an extraordinary diversity of bacteria at an OTU level. There are clusters of anisakids individuals (samples) defined by the associated bacteria which, however, are not significantly related to fish hosts or anisakid taxa. This suggests that association or relationship among bacteria in anisakids, exists without the influence of fishes or nematodes. The lack of relationships with hosts of anisakids taxa has to be expressed by the association among bacterial OTUs or other taxonomical levels which range from OTUs to the phylum level. There are significant biological structural associations of microbiota in anisakid nematodes which manifest in clusters of bacteria ranging from phylum to genus level, which could also be an indicator of fish contamination or the geographic zone of fish capture. Actinobacteria, Aquificae, Firmicutes, and Proteobacteria are the phyla whose abundance value discriminate for defining such structures.
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Affiliation(s)
- Susana C. Arcos
- Museo Nacional de Ciencias Naturales, Dpto Biodiversidad y Biología Evolutiva, CSIC, 28006 Madrid, Spain; (S.C.A.); (L.R.); (M.R.G.); (Y.J.-R.)
| | - Felipe Lira
- Centro Nacional de Biotecnología, Departamento de Biotecnología Microbiana, CSIC, 28049 Madrid, Spain; (F.L.); (J.L.M.)
| | - Lee Robertson
- Museo Nacional de Ciencias Naturales, Dpto Biodiversidad y Biología Evolutiva, CSIC, 28006 Madrid, Spain; (S.C.A.); (L.R.); (M.R.G.); (Y.J.-R.)
- Departamento de Protección Vegetal, INIA, 28040 Madrid, Spain
| | - María Rosa González
- Museo Nacional de Ciencias Naturales, Dpto Biodiversidad y Biología Evolutiva, CSIC, 28006 Madrid, Spain; (S.C.A.); (L.R.); (M.R.G.); (Y.J.-R.)
| | | | - Isabel Sánchez-Alonso
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición, CSIC, 28040 Madrid, Spain; (I.S.-A.); (M.C.)
| | - Laura Zamorano
- Servicio de Microbiología y Unidad de Investigación, Hospital Son Espases, (IdISPa), 07120 Palma de Mallorca, Spain; (L.Z.); (A.O.)
| | - Mercedes Careche
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición, CSIC, 28040 Madrid, Spain; (I.S.-A.); (M.C.)
| | - Yolanda Jiménez-Ruíz
- Museo Nacional de Ciencias Naturales, Dpto Biodiversidad y Biología Evolutiva, CSIC, 28006 Madrid, Spain; (S.C.A.); (L.R.); (M.R.G.); (Y.J.-R.)
| | - Ricardo Ramos
- Unidad de Genómica, “Scientific Park of Madrid”, Campus de Cantoblanco, 28049 Madrid, Spain;
| | - Carlos Llorens
- Biotechvana, “Scientific Park”, University of Valencia, 46980 Valencia, Spain;
| | - Miguel González-Muñoz
- Servicio de Immunología, Hospital Universitario La Paz, 28046 Madrid, Spain; (N.C.-S.); (M.G.-M.)
| | - Antonio Oliver
- Servicio de Microbiología y Unidad de Investigación, Hospital Son Espases, (IdISPa), 07120 Palma de Mallorca, Spain; (L.Z.); (A.O.)
| | - José L. Martínez
- Centro Nacional de Biotecnología, Departamento de Biotecnología Microbiana, CSIC, 28049 Madrid, Spain; (F.L.); (J.L.M.)
| | - Alfonso Navas
- Museo Nacional de Ciencias Naturales, Dpto Biodiversidad y Biología Evolutiva, CSIC, 28006 Madrid, Spain; (S.C.A.); (L.R.); (M.R.G.); (Y.J.-R.)
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Eskandari S, Etemadifar Z. Biocompatibility and radioprotection by newly characterized melanin pigment and its production from Dietzia schimae NM3 in optimized whey medium by response surface methodology. ANN MICROBIOL 2021. [DOI: 10.1186/s13213-021-01628-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Abstract
Purpose
To characterize and optimize the productivity of melanin using an extremotolerant actinobacterium, Dietzia schimae NM3, for the first time.
Methods
An extracellular brown pigment produced by D. schimae NM3 in the nutrient broth and cheese whey medium by adding L-tyrosine. The extracted melanin was analyzed by UV-visible, HPLC, and FTIR assays. The radical scavenging activity (by DPPH) and sun protection factor (SPF) of the extracted melanin were measured. The melanin cytotoxicity was assayed by MTT and chromate biosorption was measured by atomic absorption spectroscopy. Finally, melanin production by D. schimae NM3 was optimized by response surface methodology (RSM) using Box-Behnken design in the whey medium.
Result
The purified melanin showed similar peak to the standard melanin (SIGMA) at 3.5 min in HPLC, and C=O bands, NH2, CH, C-N, and aromatic groups by FTIR. The radical scavenging activity (by DPPH) and SPF of the extracted melanin were obtained 188.9% and 20.22, respectively. Using MTT assay, the melanin revealed non-toxic effect on the normal human fibroblast (HFB) cell culture. The melanin yield 790 mg l−1, and tyrosinase activity 3400 U ml−1 were obtained in the medium contained whey powder [5% (w v−1)], L-tyrosine 2.5 g l−1, CuSO4 0.013 g l−1, and pH 10.5, incubated at 32 °C for 3 days. The ANOVA results indicated significant P-value, model F-value, and probability, with insignificant lack of fit. After optimization with mono-factors, the nutrient broth came up with melanin yield as 1.2 g l−1 and tyrosinase activity as 4040 U ml−1.
Conclusion
This is the first report of melanin production by D. schimae NM3 and this natural melanin showed valuable biological properties such as high antioxidant activity and radioprotection (SPF) and the biocompatibility to human cell line.
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Grydaki N, Colbeck I, Mendes L, Eleftheriadis K, Whitby C. Bioaerosols in the Athens Metro: Metagenetic insights into the PM 10 microbiome in a naturally ventilated subway station. ENVIRONMENT INTERNATIONAL 2021; 146:106186. [PMID: 33126062 DOI: 10.1016/j.envint.2020.106186] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/30/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
To date, few studies have examined the aerosol microbial content in Metro transportation systems. Here we characterised the aerosol microbial abundance, diversity and composition in the Athens underground railway system. PM10 filter samples were collected from the naturally ventilated Athens Metro Line 3 station "Nomismatokopio". Quantitative PCR of the 16S rRNA gene and high throughput amplicon sequencing of the 16S rRNA gene and internal transcribed spacer (ITS) region was performed on DNA extracted from PM10 samples. Results showed that, despite the bacterial abundance (mean = 2.82 × 105 16S rRNA genes/m3 of air) being, on average, higher during day-time and weekdays, compared to night-time and weekends, respectively, the differences were not statistically significant. The average PM10 mass concentration on the platform was 107 μg/m3. However, there was no significant correlation between 16S rRNA gene abundance and overall PM10 levels. The Athens Metro air microbiome was mostly dominated by bacterial and fungal taxa of environmental origin (e.g. Paracoccus, Sphingomonas, Cladosporium, Mycosphaerella, Antrodia) with a lower contribution of human commensal bacteria (e.g. Corynebacterium, Staphylococcus). This study highlights the importance of both outdoor air and commuters as sources in shaping aerosol microbial communities. To our knowledge, this is the first study to characterise the mycobiome diversity in the air of a Metro environment based on amplicon sequencing of the ITS region. In conclusion, this study presents the first microbial characterisation of PM10 in the Athens Metro, contributing to the growing body of microbiome exploration within urban transit networks. Moreover, this study shows the vulnerability of public transport to airborne disease transmission.
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Affiliation(s)
- N Grydaki
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ Essex, UK
| | - I Colbeck
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ Essex, UK
| | - L Mendes
- Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety - Environmental Radioactivity Laboratory, N.C.S.R. "Demokritos", Aghia Paraskevi, 15310 Athens, Greece
| | - K Eleftheriadis
- Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety - Environmental Radioactivity Laboratory, N.C.S.R. "Demokritos", Aghia Paraskevi, 15310 Athens, Greece
| | - C Whitby
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ Essex, UK.
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Effects of rearing system and narasin on growth performance, gastrointestinal development, and gut microbiota of broilers. Poult Sci 2020; 100:100840. [PMID: 33531152 PMCID: PMC7936129 DOI: 10.1016/j.psj.2020.10.073] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/09/2020] [Accepted: 10/20/2020] [Indexed: 01/02/2023] Open
Abstract
This study was conducted to evaluate the effects of 3 rearing systems (FL: flooring litter rearing, MC: multilayer cage rearing, PN: plastic net rearing) with or without supplemental narasin on growth performance, gastrointestine development and health of broilers. A total of 2,400 one-day-old Ross 308 mixed-sex broilers (1:1 ratio of males and females) were used in a completely randomized design utilizing a 3 × 2 factorial arrangement of treatments, with 12 replicates per treatment. Each replicate for FL, MC, and PN consisted of 34 birds per floor pen, 30 birds per cage, and 36 birds per net pen, respectively, ensuring the same stocking density (12 birds/m2) across the 3 systems. Results showed that lower ADG (average daily gain), ADFI (average daily feed intake), and FCR (feed conversation ratio) observed in the MC group than those of the other 2 systems from 1 to 36 d of age (P < 0.05). Narasin inclusion in the diets decreased ADFI and FCR significantly (P < 0.05). Multilayer cage and PN rearing systems reduced the relative weight of the gizzard significantly (P < 0.05). Compared with FL, MC reduced the relative weight of the duodenum, jejunum, and ileum (P < 0.05). The mRNA expression levels of the ileal IL-1β and IFN-γ in FL were higher than those in PN and MC (P < 0.05). Narasin decreased the ileal mRNA expression of TNF-α (P < 0.05). Different rearing systems changed the ileal microflora structure of broilers. The FL system increased the ileal microbial diversity of broilers and the relative abundance of Actinobacteria. Narasin combined with MC increased the relative abundance of Proteobacteria. In conclusion, birds reared in PN had a higher body weight. The MC birds had poorer intestinal development and health condition, higher abundance of Proteobacteria, but better FCR. The FL rearing appeared to be propitious for gastrointestinal development and health. Narasin inclusion in the diets improved FCR and changed the relative abundance Proteobacteria of broilers.
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Brown JJ, Rodríguez-Ruano SM, Poosakkannu A, Batani G, Schmidt JO, Roachell W, Zima J, Hypša V, Nováková E. Ontogeny, species identity, and environment dominate microbiome dynamics in wild populations of kissing bugs (Triatominae). MICROBIOME 2020; 8:146. [PMID: 33040738 PMCID: PMC7549230 DOI: 10.1186/s40168-020-00921-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/09/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Kissing bugs (Triatominae) are blood-feeding insects best known as the vectors of Trypanosoma cruzi, the causative agent of Chagas' disease. Considering the high epidemiological relevance of these vectors, their biology and bacterial symbiosis remains surprisingly understudied. While previous investigations revealed generally low individual complexity but high among-individual variability of the triatomine microbiomes, any consistent microbiome determinants have not yet been identified across multiple Triatominae species. METHODS To obtain a more comprehensive view of triatomine microbiomes, we investigated the host-microbiome relationship of five Triatoma species sampled from white-throated woodrat (Neotoma albigula) nests in multiple locations across the USA. We applied optimised 16S rRNA gene metabarcoding with a novel 18S rRNA gene blocking primer to a set of 170 T. cruzi-negative individuals across all six instars. RESULTS Triatomine gut microbiome composition is strongly influenced by three principal factors: ontogeny, species identity, and the environment. The microbiomes are characterised by significant loss in bacterial diversity throughout ontogenetic development. First instars possess the highest bacterial diversity while adult microbiomes are routinely dominated by a single taxon. Primarily, the bacterial genus Dietzia dominates late-stage nymphs and adults of T. rubida, T. protracta, and T. lecticularia but is not present in the phylogenetically more distant T. gerstaeckeri and T. sanguisuga. Species-specific microbiome composition, particularly pronounced in early instars, is further modulated by locality-specific effects. In addition, pathogenic bacteria of the genus Bartonella, acquired from the vertebrate hosts, are an abundant component of Triatoma microbiomes. CONCLUSION Our study is the first to demonstrate deterministic patterns in microbiome composition among all life stages and multiple Triatoma species. We hypothesise that triatomine microbiome assemblages are produced by species- and life stage-dependent uptake of environmental bacteria and multiple indirect transmission strategies that promote bacterial transfer between individuals. Altogether, our study highlights the complexity of Triatominae symbiosis with bacteria and warrant further investigation to understand microbiome function in these important vectors. Video abstract.
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Affiliation(s)
- Joel J. Brown
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | | | - Anbu Poosakkannu
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Giampiero Batani
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | | | - Walter Roachell
- US Army Public Health Command-Central, JBSA Fort Sam, Houston, TX USA
| | - Jan Zima
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Václav Hypša
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Eva Nováková
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
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Khan N, Martínez-Hidalgo P, Humm EA, Maymon M, Kaplan D, Hirsch AM. Inoculation With a Microbe Isolated From the Negev Desert Enhances Corn Growth. Front Microbiol 2020; 11:1149. [PMID: 32636811 PMCID: PMC7316896 DOI: 10.3389/fmicb.2020.01149] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 05/06/2020] [Indexed: 11/13/2022] Open
Abstract
Corn (Zea mays L.) is not only an important food source, but also has numerous uses, including for biofuels, fillers for cosmetics, glues, and so on. The amount of corn grown in the U.S. has significantly increased since the 1960's and with it, the demand for synthetic fertilizers and pesticides/fungicides to enhance its production. However, the downside of the continuous use of these products, especially N and P fertilizers, has been an increase in N2O emissions and other greenhouse gases into the atmosphere as well as run-off into waterways that fuel pollution and algal blooms. These approaches to agriculture, especially if exacerbated by climate change, will result in decreased soil health as well as human health. We searched for microbes from arid, native environments that are not being used for agriculture because we reasoned that indigenous microbes from such soils could promote plant growth and help restore degraded soils. Employing cultivation-dependent methods to isolate bacteria from the Negev Desert in Israel, we tested the effects of several microbial isolates on corn in both greenhouse and small field studies. One strain, Dietzia cinnamea 55, originally identified as Planomicrobium chinense, significantly enhanced corn growth over the uninoculated control in both greenhouse and outside garden experiments. We sequenced and analyzed the genome of this bacterial species to elucidate some of the mechanisms whereby D. cinnamea 55 promoted plant growth. In addition, to ensure the biosafety of this previously unknown plant growth promoting bacterial (PGPB) strain as a potential bioinoculant, we tested the survival and growth of Caenorhabditis elegans and Galleria mellonella (two animal virulence tests) as well as plants in response to D. cinnamea 55 inoculation. We also looked for genes for potential virulence determinants as well as for growth promotion.
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Affiliation(s)
- Noor Khan
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Pilar Martínez-Hidalgo
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biology, Geology, Physics and Inorganic Chemistry, Universidad Rey Juan Carlos, Madrid, Spain
| | - Ethan A Humm
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Maskit Maymon
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Drora Kaplan
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Ann M Hirsch
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
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26
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Mpangase PT, Frost J, Ramsay M, Hazelhurst S. nf-rnaSeqMetagen: A nextflow metagenomics pipeline for identifying and characterizing microbial sequences from RNA-seq data. MEDICINE IN MICROECOLOGY 2020. [DOI: 10.1016/j.medmic.2020.100011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Madsen AM, Frederiksen MW, Jacobsen MH, Tendal K. Towards a risk evaluation of workers' exposure to handborne and airborne microbial species as exemplified with waste collection workers. ENVIRONMENTAL RESEARCH 2020; 183:109177. [PMID: 32006769 DOI: 10.1016/j.envres.2020.109177] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/16/2020] [Accepted: 01/22/2020] [Indexed: 05/24/2023]
Abstract
Bioaerosol exposure is associated with health problems. The aim of this study is to evaluate whether it is possible to assess the risks posed by waste collection workers' exposure through identification and characterization of bacterial and fungal species, to which the workers are exposed. Using MALDI-TOF MS, microorganisms in waste collection workers' exposure through air, hand, and contact with the steering wheel were identified. Fungi found in high concentrations from the workers' exposure were characterized for the total inflammatory potential (TIP), cytotoxicity, and biofilm-forming capacity. In total, 180 different bacterial and 37 different fungal species in the workers' exposure samples were identified. Some of them belong to Risk Group 2, e.g. Escherichia coli, Klebsiella oxytoca, Staphylococcus aureus, and Aspergillus fumigatus, some have been associated with occupational health problems e.g. Penicillium citrinum and P. glabrum and some are described as emerging pathogens e.g. Aureobasidium pullulans. The TIP of fungal species was dose-dependent. High TIP values were found for Penicillium italicum, P. brevicompactum, P. citrinum, and P. glabrum. Several species were cytotoxic, e.g. A. niger and P. expansum, while some, e.g. P. chrysogenum, did not affect the cell viability. Based on waste workers' average inhalation rate, they inhaled up to 2.3 × 104 cfu of A. niger, 7.4 × 104 cfu of P. expansum, and 4.0 × 106 cfu of P. italicum per work day. Some species e.g. A. niger and P. citrinum were able to form biofilm. In conclusion, the workers were exposed to several species of microorganisms of which some to varying degrees can be evaluated concerning risk. Thus, some microorganisms belong to Risk Group 2, and some are described as causing agents of occupational health problems, emerging pathogens, or intrinsically antibiotic resistant. For some other species very little is known. The TIP, cytotoxicity, and ability to form biofilm of the dominating fungi support and expand previous findings. These parameters depended on the species and the dose, thus highlighting the importance of species identification and exposure level in the risk assessment of exposure.
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Affiliation(s)
- Anne Mette Madsen
- The National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100, Copenhagen, Denmark.
| | - Margit W Frederiksen
- The National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100, Copenhagen, Denmark
| | - Mikkel Hyldeqvist Jacobsen
- The National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100, Copenhagen, Denmark
| | - Kira Tendal
- The National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100, Copenhagen, Denmark
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Schlatter DC, Paul NC, Shah DH, Schillinger WF, Bary AI, Sharratt B, Paulitz TC. Biosolids and Tillage Practices Influence Soil Bacterial Communities in Dryland Wheat. MICROBIAL ECOLOGY 2019; 78:737-752. [PMID: 30796467 DOI: 10.1007/s00248-019-01339-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Class B biosolids are used in dryland wheat (Triticum aestivum L.) production in eastern Washington as a source of nutrients and to increase soil organic matter, but little is known about their effects on bacterial communities and potential for harboring human pathogens. Moreover, conservation tillage is promoted to reduce erosion and soil degradation. We explored the impacts of biosolids or synthetic fertilizer in combination with traditional (conventional) or conservation tillage on soil bacterial communities. Bacterial communities were characterized from fresh biosolids, biosolid aggregates embedded in soil, and soil after a second application of biosolids using high-throughput amplicon sequencing. Biosolid application significantly affected bacterial communities, even 4 years after their application. Bacteria in the families Clostridiaceae, Norcardiaceae, Anaerolinaceae, Dietziaceae, and Planococcaceae were more abundant in fresh biosolids, biosolid aggregates, and soils treated with biosolids than in synthetically fertilized soils. Taxa identified as Turcibacter, Dietzia, Clostridiaceae, and Anaerolineaceae were highly abundant in biosolid aggregates in the soil and likely originated from the biosolids. In contrast, Oxalobacteriaceae, Streptomyceteaceae, Janthinobacterium, Pseudomonas, Kribbella, and Bacillus were rare in the fresh biosolids, but relatively abundant in biosolid aggregates in the soil, and probably originated from the soil to colonize the substrate. However, tillage had relatively minor effects on bacterial communities, with only a small number of taxa differing in relative abundance between traditional and conventional tillage. Although biosolid-associated bacteria persisted in soil, potentially pathogenic taxa were extremely rare and no toxin genes for key groups (Salmonella, Clostridium) were detectable, suggesting that although fecal contamination was apparent via indicator taxa, pathogen populations had declined to low levels. Thus, biosolid amendments had profound effects on soil bacterial communities both by introducing gut- or digester-derived bacteria and by enriching potentially beneficial indigenous soil populations.
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Affiliation(s)
- Daniel C Schlatter
- Wheat Health, Genetics and Quality Research Unit, USDA-ARS, Pullman, WA, 99164, USA
| | - Narayan C Paul
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Devendra H Shah
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - William F Schillinger
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Andy I Bary
- Puyallup Research and Extension Center, Washington State University, Puyallup, WA, 98371, USA
| | - Brenton Sharratt
- Northwest Sustainable Agroecosystems Research Unit, USDA-ARS, Pullman, WA, 99164, USA
| | - Timothy C Paulitz
- Wheat Health, Genetics and Quality Research Unit, USDA-ARS, Pullman, WA, 99164, USA.
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Antibiotic resistance genes in the Actinobacteria phylum. Eur J Clin Microbiol Infect Dis 2019; 38:1599-1624. [PMID: 31250336 DOI: 10.1007/s10096-019-03580-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/01/2019] [Indexed: 02/07/2023]
Abstract
The Actinobacteria phylum is one of the oldest bacterial phyla that have a significant role in medicine and biotechnology. There are a lot of genera in this phylum that are causing various types of infections in humans, animals, and plants. As well as antimicrobial agents that are used in medicine for infections treatment or prevention of infections, they have been discovered of various genera in this phylum. To date, resistance to antibiotics is rising in different regions of the world and this is a global health threat. The main purpose of this review is the molecular evolution of antibiotic resistance in the Actinobacteria phylum.
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30
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Waltmann A, Willcox AC, Balasubramanian S, Borrini Mayori K, Mendoza Guerrero S, Salazar Sanchez RS, Roach J, Condori Pino C, Gilman RH, Bern C, Juliano JJ, Levy MZ, Meshnick SR, Bowman NM. Hindgut microbiota in laboratory-reared and wild Triatoma infestans. PLoS Negl Trop Dis 2019; 13:e0007383. [PMID: 31059501 PMCID: PMC6522061 DOI: 10.1371/journal.pntd.0007383] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 05/16/2019] [Accepted: 04/10/2019] [Indexed: 12/14/2022] Open
Abstract
Triatomine vectors transmit Trypanosoma cruzi, the etiological agent of Chagas disease in humans. Transmission to humans typically occurs when contaminated triatomine feces come in contact with the bite site or mucosal membranes. In the Southern Cone of South America, where the highest burden of disease exists, Triatoma infestans is the principal vector for T. cruzi. Recent studies of other vector-borne illnesses have shown that arthropod microbiota influences the ability of infectious agents to colonize the insect vector and transmit to the human host. This has garnered attention as a potential control strategy against T. cruzi, as vector control is the main tool of Chagas disease prevention. Here we characterized the microbiota in T. infestans feces of both wild-caught and laboratory-reared insects and examined the relationship between microbial composition and T. cruzi infection using highly sensitive high-throughput sequencing technology to sequence the V3-V4 region of the 16S ribosomal RNA gene on the MiSeq Illumina platform. We collected 59 wild (9 with T. cruzi infection) and 10 lab-reared T. infestans (4 with T. cruzi infection) from the endemic area of Arequipa, Perú. Wild T. infestans had greater hindgut bacterial diversity than laboratory-reared bugs. Microbiota of lab insects comprised a subset of those identified in their wild counterparts, with 96 of the total 124 genera also observed in laboratory-reared insects. Among wild insects, variation in bacterial composition was observed, but time and location of collection and development stage did not explain this variation. T. cruzi infection in lab insects did not affect α- or β-diversity; however, we did find that the β-diversity of wild insects differed if they were infected with T. cruzi and identified 10 specific taxa that had significantly different relative abundances in infected vs. uninfected wild T. infestans (Bosea, Mesorhizobium, Dietzia, and Cupriavidus were underrepresented in infected bugs; Sporosarcina, an unclassified genus of Porphyromonadaceae, Nestenrenkonia, Alkalibacterium, Peptoniphilus, Marinilactibacillus were overrepresented in infected bugs). Our findings suggest that T. cruzi infection is associated with the microbiota of T. infestans and that inferring the microbiota of wild T. infestans may not be possible through sampling of T. infestans reared in the insectary. Chagas disease in humans is caused by the parasite Trypanosoma cruzi and it is endemic to the Americas. Poor populations are most at risk. The parasite infects an estimated six million people of 21 endemic countries in the Americas, with 30,000 new infections yearly. The main mode of transmission is vector-borne by triatomine bugs, which tend to live in close association with humans. The main Chagas disease vector in the Southern Cone of South America, where the highest burden of disease exists, is Triatoma infestans. As blood-sucking insects, triatomines become infected when they bite a T. cruzi-positive human and once infected they transmit the parasites in their feces. Controlling the vector populations is the main strategy of Chagas disease transmission reduction efforts. Microbiota-mediated methods to control this vector-borne disease are now being explored to determine whether microbes typically found in the vectors’ gut have a detrimental effect on T. cruzi and how they may be used to modify the vector and curb the ability for T. cruzi to be transmitted to humans. To advance this new field, we first must gain better knowledge of the gut microbiota of triatomines. Our study is the first to use sensitive high-throughput methods to study the gut microbes of T. infestans, using both laboratory-reared and wild insects. We have found that the microbial composition of T. infestans in the laboratory does not reflect the complete collection of gut microbes of wild T. infestans and inferring the gut microbiota profile of wild insects through studying lab insects alone may not be possible. We also found evidence that in wild insects T. cruzi affects the composition of the gut microbiota and identified some bacterial taxa which may be important in modulating the T.infestans-T.cruzi relationship.
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Affiliation(s)
- Andreea Waltmann
- Institute for Global Health and Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
| | - Alexandra C. Willcox
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sujata Balasubramanian
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Katty Borrini Mayori
- Zoonotic Disease Research Laboratory, Unidad de Una Salud, Universidad Peruana Cayetano Heredia, Arequipa, Perú
| | - Sandra Mendoza Guerrero
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Renzo S. Salazar Sanchez
- Zoonotic Disease Research Laboratory, Unidad de Una Salud, Universidad Peruana Cayetano Heredia, Arequipa, Perú
| | - Jeffrey Roach
- Microbiome Core Facility, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Carlos Condori Pino
- Zoonotic Disease Research Laboratory, Unidad de Una Salud, Universidad Peruana Cayetano Heredia, Arequipa, Perú
| | - Robert H. Gilman
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Caryn Bern
- Department of Epidemiology and Biostatistics, School of Medicine, University of California-San Francisco, San Francisco, California, United States of America
| | - Jonathan J. Juliano
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Michael Z. Levy
- Department of Biostatistics, Epidemiology & Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Steven R. Meshnick
- Institute for Global Health and Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Natalie M. Bowman
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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A time travel story: metagenomic analyses decipher the unknown geographical shift and the storage history of possibly smuggled antique marble statues. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-1446-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Bacterial diversity obtained by culturable approaches in the gut of Glossina pallidipes population from a non sleeping sickness focus in Tanzania: preliminary results. BMC Microbiol 2018; 18:164. [PMID: 30470192 PMCID: PMC6251091 DOI: 10.1186/s12866-018-1288-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Glossina pallidipes is a haematophagous insect that serves as a cyclic transmitter of trypanosomes causing African Trypanosomiasis (AT). To fully assess the role of G. pallidipes in the epidemiology of AT, especially the human form of the disease (HAT), it is essential to know the microbial diversity inhabiting the gut of natural fly populations. This study aimed to examine the diversity of G. pallidipes fly gut bacteria by culture-dependent approaches. RESULTS 113 bacterial isolates were obtained from aerobic and anaerobic microorganisms originating from the gut of G. pallidipes. 16S rDNA of each isolate was PCR amplified and sequenced. The overall majority of identified bacteria belonged in descending order to the Firmicutes (86.6%), Actinobacteria (7.6%), Proteobacteria (5.5%)and Bacteroidetes (0.3%). Diversity of Firmicutes was found higher when enrichments and isolation were performed under anaerobic conditions than aerobic ones. Experiments conducted in the absence of oxygen (anaerobiosis) led to the isolation of bacteria pertaining to four phyla (83% Firmicutes, 15% Actinobacteria, 1% Proteobacteria and 0.5% Bacteroidetes, whereas those conducted in the presence of oxygen (aerobiosis) led to the isolation of bacteria affiliated to two phyla only (90% Firmicutes and 10% Proteobacteria). Phylogenetic analyses placed these isolates into 11 genera namely Bacillus, Acinetobacter, Mesorhizobium, Paracoccus, Microbacterium, Micrococcus, Arthrobacter, Corynobacterium, Curtobacterium, Vagococcus and Dietzia spp.which are known to be either facultative anaerobes, aerobes, or even microaerobes. CONCLUSION This study shows that G. pallidipes fly gut is an environmental reservoir for a vast number of bacterial species, which are likely to be important for ecological microbial well being of the fly and possibly on differing vectorial competence and refractoriness against AT epidemiology.
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Identification of Dietzia Species in a Patient with Endophthalmitis following Penetrating Injury with Retained Intraocular Metallic Foreign Body. Case Rep Infect Dis 2018; 2018:3027846. [PMID: 30356339 PMCID: PMC6176285 DOI: 10.1155/2018/3027846] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/27/2018] [Indexed: 11/24/2022] Open
Abstract
To the best of our knowledge, we report the first case of Dietzia species in a patient with endophthalmitis. A 47-year-old man presented to the ophthalmology department with decreased vision, redness, and minimal pain in his right eye after a foreign body struck his eye following working using a hammer and chisel. Broad-spectrum polymerase chain reaction (PCR) and deoxyribonucleic acid (DNA) sequencing targeting 16S ribosomal ribonucleic acid-(rRNA-) encoding gene on an undiluted vitreous sample revealed 100% identity with GenBank sequences of Dietzia species including D. natronolimnaea, D. dagingensis, and D. cercidiphylli. The culture of the vitreous samples demonstrated the growth of Gram-positive cocci and polymorphic rods. The isolate from the culture was identified as D. natronolimnaea using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS). The combination of surgical and medical treatment (pars plana vitrectomy and systemic and topical antibiotics) eradicated the infection successfully.
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Li G, Gao P, Zhi B, Fu B, Gao G, Chen Z, Gao M, Wu M, Ma T. The relative abundance of alkane-degrading bacteria oscillated similarly to a sinusoidal curve in an artificial ecosystem model from oil-well products. Environ Microbiol 2018; 20:3772-3783. [DOI: 10.1111/1462-2920.14382] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/19/2018] [Accepted: 08/10/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Guoqiang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
- Department of Microbiology and Plant Biology; University of Oklahoma; Norman OK USA
| | - Peike Gao
- College of Life Sciences; Qufu Normal University; Qufu People's Repubic of China
| | - Bo Zhi
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Bing Fu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Ge Gao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Zhaohui Chen
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Mengli Gao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Mengmeng Wu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
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Koszutski M, Faure M, Guillaumot A, Gomez E, Mercy M, Chabot F, Chaouat A. [Tunnelled central venous catheter infection during treatment with epoprostenol]. Rev Mal Respir 2018; 35:324-327. [PMID: 29602480 DOI: 10.1016/j.rmr.2017.03.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 03/31/2017] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Pulmonary arterial hypertension is a pulmonary vascular disease with a poor prognosis. Continuous intravenous treatment with prostacyclin analogues requires the placement of a tunnelled catheter. The occurrence of catheter-related infections in this context is unusual due to the alkaline pH of the prostacyclin analogue solutions. OBSERVATION A 50-year-old patient with inherited pulmonary artery hypertension, treated with bosentan, sildenafil and epoprostenol, experienced generalized malaise associated with a weight loss of 9kg over a 12-month period without evidence of a source of infection or malignancy. There was no evidence of hemodynamic disturbance. The diagnosis was made after 1 year of follow-up, when the patient presented with a 38° fever and a biological inflammatory syndrome. Repeated peripheral blood cultures were positive for Dietzia, an alkalophilic coryneform bacillus. The patient's condition responded favourably to antibiotic therapy. CONCLUSION Infection of a tunneled intravenous catheter should be considered in the case of non-specific symptoms or where there is evidence of sepsis, in patients treated with intravenous prostacyclin analogues administered intravenously. In this context, the laboratory should be warned to search for slow-growing organisms.
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Affiliation(s)
- M Koszutski
- Pôle des spécialités médicales, département de pneumologie, CHU de Nancy, rue du Morvan, 54500 Vandœuvre-lès-Nancy, France.
| | - M Faure
- Pôle des spécialités médicales, département de pneumologie, CHU de Nancy, rue du Morvan, 54500 Vandœuvre-lès-Nancy, France
| | - A Guillaumot
- Pôle des spécialités médicales, département de pneumologie, CHU de Nancy, rue du Morvan, 54500 Vandœuvre-lès-Nancy, France
| | - E Gomez
- Pôle des spécialités médicales, département de pneumologie, CHU de Nancy, rue du Morvan, 54500 Vandœuvre-lès-Nancy, France
| | - M Mercy
- Pôle des spécialités médicales, département de pneumologie, CHU de Nancy, rue du Morvan, 54500 Vandœuvre-lès-Nancy, France
| | - F Chabot
- Pôle des spécialités médicales, département de pneumologie, CHU de Nancy, rue du Morvan, 54500 Vandœuvre-lès-Nancy, France
| | - A Chaouat
- Pôle des spécialités médicales, département de pneumologie, CHU de Nancy, rue du Morvan, 54500 Vandœuvre-lès-Nancy, France; INGRES, EA 7298, université de lorraine, 54500 Vandœuvre-lès-Nancy, France
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Isolation and characterization of microorganisms and volatiles associated with Moroccan saffron during different processing treatments. Int J Food Microbiol 2018; 273:43-49. [PMID: 29574333 DOI: 10.1016/j.ijfoodmicro.2018.03.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/17/2018] [Accepted: 03/19/2018] [Indexed: 11/22/2022]
Abstract
Saffron may be spoiled by a variety of microorganisms during cultivation, harvesting, and post harvesting. As saffron can be dried and stored in different ways, this preliminary study explored the natural microbiota present in Moroccan saffron when subjected to different drying techniques. An analysis of the carotenoid-derived volatiles present in the saffron was also carried out. The culturable microbiota of the saffron samples dried using different methods, namely in the shade (also called natural), in the sun, or in the oven, were studied using classical and molecular approaches. The effect of the drying methods on head-space chemical volatiles was also determined. Eighty-two isolates grown in the different culture media were chosen from the colonies, and genotype analysis grouped the microorganisms into 58 clusters, revealing a wide diversity. Out of the 82 isolates, 75 belonged to the Bacillaceae family. The other isolates were distributed within the Dietziaceae, Paenibacillaceae and Carnobacteriaceae families. The dominant species was Bacillus simplex, which was detected in all samples, regardless of the drying method used. Lysinibacillus macroides was dominant in the sun-dried saffron. No pathogens were isolated, but an isolate belonging to Dietzia maris, a potential human pathogenic species, was detected. The biodiversity indexes were linked to the drying method and generally decreased as the intensity of the treatment increased. The results of this preliminary work show that the different drying methods strongly influenced the microbiota and affect the saffron volatile profile. Further analysis will be needed to determine possible effects of selected microbiota on saffron volatiles.
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Montoya-Porras LM, Omar TC, Alzate JF, Moreno-Herrera CX, Cadavid-Restrepo GE. 16S rRNA gene amplicon sequencing reveals dominance of Actinobacteria in Rhodnius pallescens compared to Triatoma maculata midgut microbiota in natural populations of vector insects from Colombia. Acta Trop 2018; 178:327-332. [PMID: 29154947 DOI: 10.1016/j.actatropica.2017.11.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 10/19/2017] [Accepted: 11/14/2017] [Indexed: 01/19/2023]
Abstract
Chagas disease affects more than 6 million people in Latin America, it is a parasitic disease caused by the protozoan Trypanosoma cruzi, which is transmitted mainly by bloodsucking insects of the Triatominae subfamily. Studies on microbial communities that inhabit the insect gut are important to understanding their role in the parasite transmission and development. The present work aims to evaluate the gut bacterial composition of natural populations of triatomine species from Vichada and Magdalena, administrative states called departments in Colombia, using high-throughput sequencing technologies. The insects were collected from housing peridomestic area and Attalea butyracea palms; they were identified by conventional taxonomy as Triatoma maculata and Rhodnius pallescens, and their guts were dissected under aseptic conditions in order to obtain total DNA. After DNA quality confirmation, the sequencing of the V4 region of 16S rRNA gene was carried out using the Illumina platform MiSeq. The results showed that 13 predominant bacterial genera were present in both species, being Burkholderia, Gordonia, and Ralstonia, the most prevailing bacterial genera. Furthermore, representative genera of each species were found. Williamsia and Kocuria were the most common in R. pallescens; and Dietzia, Aeromonas, and Pelomonas were only observed in T. maculata samples. This is the first study of microbiota associated with these triatomine species using massive sequencing methods The approach allowed inferring the presence of a dominant population of bacteria according to the triatomine species in Colombia, which may suggest a strong association between microbiota and their host.
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Braun DR, Chevrette MG, Acharya D, Currie CR, Rajski SR, Ritchie KB, Bugni TS. Complete Genome Sequence of Dietzia sp. Strain WMMA184, a Marine Coral-Associated Bacterium. GENOME ANNOUNCEMENTS 2018; 6:e01582-17. [PMID: 29437114 PMCID: PMC5794961 DOI: 10.1128/genomea.01582-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 01/02/2018] [Indexed: 01/25/2023]
Abstract
Dietzia sp. strain WMMA184 was isolated from the marine coral Montastraea faveolata as part of ongoing drug discovery efforts. Analysis of the 4.16-Mb genome provides information regarding interspecies interactions as it pertains to the regulation of secondary metabolism and natural product biosynthesis potential.
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Affiliation(s)
- Doug R Braun
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Marc G Chevrette
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Deepa Acharya
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Scott R Rajski
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kim B Ritchie
- The University of South Carolina-Beaufort, Beaufort, South Carolina, USA
| | - Tim S Bugni
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Hvidsten I, Mjøs SA, Holmelid B, Bødtker G, Barth T. Lipids of Dietzia sp. A14101. Part I: A study of the production dynamics of surface-active compounds. Chem Phys Lipids 2017; 208:19-30. [DOI: 10.1016/j.chemphyslip.2017.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 08/06/2017] [Accepted: 08/14/2017] [Indexed: 11/25/2022]
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Guo A, Gu J, Wang X, Zhang R, Yin Y, Sun W, Tuo X, Zhang L. Effects of superabsorbent polymers on the abundances of antibiotic resistance genes, mobile genetic elements, and the bacterial community during swine manure composting. BIORESOURCE TECHNOLOGY 2017; 244:658-663. [PMID: 28813691 DOI: 10.1016/j.biortech.2017.08.016] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/29/2017] [Accepted: 08/04/2017] [Indexed: 06/07/2023]
Abstract
Superabsorbent polymers (SAPs) are considered suitable amendments for reducing the selection pressure due to heavy metals and the abundances of antibiotic resistance genes (ARGs) during composting. In this study, three SAP (sodium polyacrylate) levels (0, 5, and 15mgkg-1 of compost) were applied and their effects on the abundances of ARGs, mobile genetic elements (MGEs), and the bacterial community were investigated. After composting, the abundances of ARGs and MGEs decreased to different extent, where the removal efficiencies for tetW, dfrA7, ermX, aac(6')-ib-cr and MGEs exceeded 90%. The high SAP concentration significantly reduced the abundances of ARGs and MGEs, and changed the microbial community. Redundancy analysis indicated that the moisture content mainly explained the changes in ARGs and MGEs. Network analysis determined the potential hosts of ARGs and MGEs, and their co-occurrence. The results suggested that applying 15mgkg-1 SAP is appropriate for reducing ARGs in compost.
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Affiliation(s)
- Aiyun Guo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiaojuan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ranran Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanan Yin
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei Sun
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaxia Tuo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Li Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
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Hvidsten I, Mjøs SA, Bødtker G, Barth T. Lipids of Dietzia sp. A14101. Part II: A study of the dynamics of the release of surface active compounds by Dietzia sp. A14101 into the medium. Chem Phys Lipids 2017; 208:31-42. [PMID: 28837792 DOI: 10.1016/j.chemphyslip.2017.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 08/06/2017] [Accepted: 08/14/2017] [Indexed: 11/26/2022]
Abstract
Dietzia sp. A14101 isolated from an oil reservoir model column was found to induce a strong decrease of the interfacial tension (IFT) in hydrocarbon-water mixtures in the presence of the intact bacterial cells (Kowalewski et al., 2005). The strain was shown to be able to degrade a wide range of hydrocarbon substrates (Bødtker et al., 2009). Further studies showed that the surface-active compounds tentatively identified as glycolipids were produced by Dietzia sp. A14101 on non- and water-immiscible -hydrocarbon substrates, Part I (Hvidsten et al., 2017). The results suggested that biosurfactant (BS) was a mixture of several isomers. The study presented here is aimed to investigate whether BS are secreted into the aqueous medium, and if so, then at which phase of the culture growth and in which amounts - the dynamics of the BS release in incubations on water-immiscible hydrocarbons. Two methods of BS extraction from the medium were attempted and compared: a liquid-liquid extraction (LLE) and precipitation by acid. For qualitative and semi-quantitative assessment, gas chromatography-mass spectrometry (GC/MS), thin-layer chromatography (TLC), liquid chromatography-mass spectrometry (LC-MS), surface tension measurements (SFT), emulsification (E24) and oil-spreading tests were employed. The results indicated that BS only partially were secreted into the medium. Detectable amounts of glycolipids in media were first identified during the exponential growth phase. However, only a slight decrease of SFT was observed in the cell-free medium. The emulsification index values of the sampled material were lower than those reported for related strains. The results suggested that most of the BS produced by Dietzia sp. A14101 remains cell-bound during the culture development in a batch mode and only a narrow range of the BS isomers can be detected in small amounts in media.
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Affiliation(s)
- Ina Hvidsten
- Department of Chemistry, University of Bergen, Allégaten 41, 5007 Bergen, Norway.
| | - Svein Are Mjøs
- Department of Chemistry, University of Bergen, Allégaten 41, 5007 Bergen, Norway
| | - Gunhild Bødtker
- Uni Research CIPR, Uni Research, P.O. Box 7810, 5020 Bergen, Norway
| | - Tanja Barth
- Department of Chemistry, University of Bergen, Allégaten 41, 5007 Bergen, Norway
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Abstract
The group of Gram-positive bacillary organisms broadly known as "aerobic actinomycetes" consists of heterogeneous and taxonomically divergent genera. They are found in a wide variety of natural and man-made environments but are rarely considered a part of the normal human flora, with infections normally originating from exogenous sources. An extensive number of genera have been described, but only a minority of these has been associated with human or veterinary health. The association with human disease is usually of an opportunistic nature, either through accidental means of inoculation or through involvement with immunocompromising conditions in the host. They cause a wide spectrum of diseases in humans, which may differ greatly between the genera and even between species, but which also may have a great amount of overlap. The occurrence of such infections is probably greater than appreciated, since many may go unrecognized. Etiologic prevalence of specific genera and species varies geographically within the United States and worldwide. Traditional phenotypic identification methods for separation of the many genera and species of aerobic actinomycetes have found great difficulties. Recent use of chemotaxonomic analyses and emerging technologies such as molecular analysis of nucleic acids, and more recently proteomics for identification to the genus/species level, has provided a far more robust technique to understand the organisms' relatedness, distribution, epidemiology, and pathogenicity in humans.
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Comparison of the Vitek MS and Bruker Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Systems for Identification of Rhodococcus equi and Dietzia spp. J Clin Microbiol 2017; 55:2255-2260. [PMID: 28490491 DOI: 10.1128/jcm.00377-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/05/2017] [Indexed: 12/11/2022] Open
Abstract
Rhodococcus equi causes pyogranulomatous pneumonia in domesticated animals and immunocompromised humans. Dietzia spp. are environmental bacteria that have rarely been associated with human infections. R. equi and Dietzia spp. are closely related actinomycetes. Phenotypic discrimination between R. equi and Dietzia on the basis of their Gram stain morphology and colony appearance is problematic. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a fast, reliable, and cost-effective method for identification of a wide variety of microorganisms. We have evaluated the performance of Bruker Biotyper versus that of Vitek MS for identification of a collection of 154 isolates identified at the source as R. equi that includes isolates belonging to the genus Dietzia PCR amplification of the choE gene, encoding a cholesterol oxidase, and 16S rRNA sequencing were considered the reference methods for R. equi identification. Biotyper identified 131 (85.1%) of the 154 isolates at the species level, and this figure increased to 152 (98.7%) when the species cutoff was reduced from a score of ≥2.000 to ≥1.750. Vitek MS correctly identified at the species level 130 (84.4%) isolates as long as bacteria were extracted with ethanol but only 35 (22.7%) isolates when samples were prepared by direct extraction from colonies. The two systems allowed differentiation between R. equi and Dietzia spp., but identification of all Dietzia sp. isolates at the species level needed sequencing of the 16S rRNA gene.
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Gusain P, Paliwal R, Singh V. Rhizoremediation of cadmium-contaminated soil associated with hydroxamate siderophores isolated from Cd-resistant plant growth-promoting Dietzia maris and Lysinibacillus strains. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2017; 19:290-299. [PMID: 27592870 DOI: 10.1080/15226514.2016.1225281] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In search of multitrait plant growth-promoting (PGP) inoculants, we introduced two cadmium-resistant bacterial strains, C4 (PG), C5 (WB), and their consortium C6 (PG × WB) isolated from metal-contaminated industrial waste-fed canal near West Bengal. The test isolates were biochemically characterized and screened in vitro for siderophore production. The infrared spectra revealed the hydroxamate nature of the siderophore produced. Further in green house, siderophore-based seed inoculation with selected PGP isolates exhibited stimulatory effects on seed germination (up to 85.4%), chlorophyll index (22.9 spad unit), shoot and root length (70% and 62.7%), tiller numbers (38.82%), spikelet numbers (52.2%), straw yield (62.2%), grain yield (76.1%), total dry matter of root and shoot (55.56% and 64.4%, respectively), and grain yields (76.1%) of tested wheat cultivars. The 16S rRNA sequencing identified strain PG and WB as Dietzia maris and Lysinibacillus sp. strains. Furthermore, inoculation of C6 (consortium) in both cultivar UP-2565 and KS-227 showed maximum Cd sorption capacity in roots (38.3% and 67.1%) and shoots (68.4% and 67.5%), respectively. Both the strains and their consortium showed a great potential to increase the growth and yield of wheat cultivars, which can also be utilized for rhizoremediation process.
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Affiliation(s)
- Poonam Gusain
- a Department of Microbiology , G. B. Pant University of Agriculture and Technology , Pantnagar , India
- b Patanjali Herbal Research Department , Patanjali Yogpeeth, Maharshi Dayanand Gram , Haridwar , India
| | - Rashmi Paliwal
- c Institute of Environmental Studies, Kurukshetra University , Kurukshetra , India
| | - Vir Singh
- d Department of Environmental Sciences , G. B. Pant University of Agriculture and Technology , Pantnagar , India
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Floc Formation Reduces the pH Stress Experienced by Microorganisms Living in Alkaline Environments. Appl Environ Microbiol 2017; 83:AEM.02985-16. [PMID: 28087527 DOI: 10.1128/aem.02985-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/05/2017] [Indexed: 11/20/2022] Open
Abstract
The survival of microorganisms within a cementitious geological disposal facility for radioactive wastes heavily depends on their ability to survive the calcium-dominated, hyperalkaline conditions resulting from the dissolution of the cementitious materials. The results from this study show that the formation of flocs, composed of a complex mixture of extracellular polymeric substances (EPS), provides protection against alkaline pH values up to 13.0. The flocs were dominated by Alishewanella and Dietzia spp., producing a mannose-rich carbohydrate fraction incorporating extracellular DNA, resulting in Ca2+ sequestration. EPS provided a ∼10-μm thick layer around the cells within the center of the flocs, which were capable of growth at pH values of 11.0 and 11.5, maintaining internal pH values of 10.4 and 10.7, respectively. Microorganisms survived at a pH of 12.0, where an internal floc pH of 11.6 was observed, as was a reduced associated biomass. We observed limited floc survival (<2 weeks) at a pH of 13.0. This study demonstrates that flocs maintain lower internal pHs in response to the hyperalkaline conditions expected to occur within a cementitious geological disposal facility for radioactive wastes and indicates that floc communities within such a facility can survive at pHs up to 12.0.IMPORTANCE The role of extracellular polymeric substances (EPS) in the survival of microorganisms in hyperalkaline conditions is poorly understood. Here, we present the taxonomy, morphology, and chemical characteristics of an EPS-based microbial floc, formed by a consortium isolated from an anthropogenic hyperalkaline site. Short-term (<2 weeks) survival of the flocs at a pH of 13 was observed, with indefinite survival observed at a pH of 12.0. Measurements from micro-pH electrodes (10-μm-diameter tip) demonstrated that flocs maintain lower internal pHs in response to hyperalkaline conditions (pH 11.0, 11.5, and 12.0), demonstrating that floc formation and EPS production are survival strategies under hyperalkaline conditions. The results indicate how microbial communities may survive and propagate within the hyperalkaline environment that is expected to prevail in a cementitious geological disposal facility for radioactive wastes; the results are also relevant to the wider extremophile community.
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Das A, Singh T, LokaBharathi PA, Dhakephalkar PK, Mallik S, Kshirsagar PR, Khadge NH, Nath BN, Bhattacharya S, Dagar AK, Kaur P, Ray D, Shukla AD, Fernandes CEG, Fernandes SO, Thomas TRA, S S M, Mourya BS, Meena RM. Astrobiological implications of dim light phototrophy in deep-sea red clays. LIFE SCIENCES IN SPACE RESEARCH 2017; 12:39-50. [PMID: 28212707 DOI: 10.1016/j.lssr.2017.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 01/20/2017] [Indexed: 06/06/2023]
Abstract
Red clays of Central Indian Basin (CIB) under influence of trace of Rodriguez Triple Junction exhibited chemoautotrophy, low temperature hydrothermal alterations and photoautotrophic potential. Seamount flank TVBC-08, hosting such signatures revealed dominance of aerobic anoxygenic phototroph Erythrobacter, with 93% of total 454 pyrosequencing tags. Subsequently, enrichments for both aerobic (Erythrobacter) and anaerobic anoxygenic phototrophs (green and purple sulphur bacteria) under red and white LED light illumination, with average irradiance 30.66Wm-2, were attempted for three red-clay sediment cores. Successful enrichments were obtained after incubation for c.a. 120 days at 4°± 2°C and 25°± 2°C, representing ambient psychrophilic and low temperature hydrothermal alteration conditions respectively. During hydrothermal cooling, a microbial succession from anaerobic chemolithotrophy to oxygenic photoautotrophy through anaerobic/aerobic anoxygenic phototrophic microbes is indicated. Spectral absorbance patterns of the methanol extracted cell pellets showed peaks corresponding to metal sulphide precipitations, the Soret band of chlorosome absorbance by photosystem II and absence of peaks at Qy transition band. Dendritic nano-structures of metal sulphides are common in these sediments and are comparable with other sulphidic paleo-marine Martian analogues. Significant blue and redshifts have been observed for the experimental samples relative to the un-inoculated medium. These observations indicate the propensity of metal-sulphide deposits contributing to chemiluminiscence supporting the growth of phototrophs at least partially, in the otherwise dark abyss. The effects of other geothermal heat and light sources are also under further consideration. The potential of phototrophic microbial cells to exhibit Doppler shift in absorbance patterns is significant towards understanding planetary microbial habitability. Planetary desiccation could considerably influence Doppler effects and consequently spectral detection techniques exo-planetary microbial life.
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Affiliation(s)
- Anindita Das
- Agharkar Research Institute-Maharashtra Association for the Cultivation of Science (MACS), G.G. Agarkar Road, Pune-411004, Maharastra, India; Council of Scientific and Industrial Research-National Institute of Oceanography, Dona Paula-403004, Goa, India.
| | - Tanya Singh
- Council of Scientific and Industrial Research-National Institute of Oceanography, Dona Paula-403004, Goa, India; Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu, Okinawa 905-0277, Japan
| | - P A LokaBharathi
- Council of Scientific and Industrial Research-National Institute of Oceanography, Dona Paula-403004, Goa, India
| | - Prashant K Dhakephalkar
- Agharkar Research Institute-Maharashtra Association for the Cultivation of Science (MACS), G.G. Agarkar Road, Pune-411004, Maharastra, India
| | - Sweta Mallik
- Agharkar Research Institute-Maharashtra Association for the Cultivation of Science (MACS), G.G. Agarkar Road, Pune-411004, Maharastra, India
| | - Pranav R Kshirsagar
- Agharkar Research Institute-Maharashtra Association for the Cultivation of Science (MACS), G.G. Agarkar Road, Pune-411004, Maharastra, India
| | - N H Khadge
- Council of Scientific and Industrial Research-National Institute of Oceanography, Dona Paula-403004, Goa, India
| | - B Nagender Nath
- Council of Scientific and Industrial Research-National Institute of Oceanography, Dona Paula-403004, Goa, India
| | - Satadru Bhattacharya
- Space Application Centre- Indian Space Research Organisation (SAC-ISRO), #4361, Satellite Road, Ambawadi Vistar P. O., Ahmedabad - 380 015, Gujarat, India
| | - Aditya Kumar Dagar
- Space Application Centre- Indian Space Research Organisation (SAC-ISRO), #4361, Satellite Road, Ambawadi Vistar P. O., Ahmedabad - 380 015, Gujarat, India
| | - Prabhjot Kaur
- Space Application Centre- Indian Space Research Organisation (SAC-ISRO), #4361, Satellite Road, Ambawadi Vistar P. O., Ahmedabad - 380 015, Gujarat, India
| | - Dwijesh Ray
- Physical Research Laboratory, Thaltej, Ahmedabad-380054, Gujrat, India
| | - Anil D Shukla
- Physical Research Laboratory, Thaltej, Ahmedabad-380054, Gujrat, India
| | - Christabelle E G Fernandes
- Council of Scientific and Industrial Research-National Institute of Oceanography, Dona Paula-403004, Goa, India
| | - Sheryl O Fernandes
- Council of Scientific and Industrial Research-National Institute of Oceanography, Dona Paula-403004, Goa, India; National Centre for Antarctic and Ocean Research, Headland Sada, Vasco-da-Gama 403804, Goa, India
| | - Tresa Remya A Thomas
- Council of Scientific and Industrial Research-National Institute of Oceanography, Dona Paula-403004, Goa, India
| | - Mamatha S S
- Council of Scientific and Industrial Research-National Institute of Oceanography, Dona Paula-403004, Goa, India
| | - Babu Shashikant Mourya
- Council of Scientific and Industrial Research-National Institute of Oceanography, Dona Paula-403004, Goa, India
| | - Ram Murti Meena
- Council of Scientific and Industrial Research-National Institute of Oceanography, Dona Paula-403004, Goa, India
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Identification of Dietzia spp. from Cardiac Tissue by 16S rRNA PCR in a Patient with Culture-Negative Device-Associated Endocarditis: A Case Report and Review of the Literature. Case Rep Infect Dis 2016; 2016:8935052. [PMID: 28101387 PMCID: PMC5215629 DOI: 10.1155/2016/8935052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 10/25/2016] [Accepted: 12/05/2016] [Indexed: 11/18/2022] Open
Abstract
The genus Dietzia was recently distinguished from other actinomycetes such as Rhodococcus. While these organisms are known to be distributed widely in the environment, over the past decade several novel species have been described and isolated from human clinical specimens. Here we describe the identification of Dietzia natronolimnaea/D. cercidiphylli by PCR amplification and sequencing of the 16S rRNA encoding gene from cardiac tissue in a patient with culture-negative device-associated endocarditis.
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Skladnev DA, Mulyukin AL, Filippova SN, Kulikov EE, Letarova MA, Yuzbasheva EA, Karnysheva EA, Brushkov AV, Gal’chenko VF. Modeling of dissemination of microbial cells and phages from the sites of permafrost thawing. Microbiology (Reading) 2016. [DOI: 10.1134/s0026261716050167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Budachetri K, Gaillard D, Williams J, Mukherjee N, Karim S. A snapshot of the microbiome of Amblyomma tuberculatum ticks infesting the gopher tortoise, an endangered species. Ticks Tick Borne Dis 2016; 7:1225-1229. [PMID: 27460902 DOI: 10.1016/j.ttbdis.2016.07.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 07/18/2016] [Accepted: 07/18/2016] [Indexed: 02/01/2023]
Abstract
The gopher tortoise tick, Amblyomma tuberculatum, has a unique relationship with the gopher tortoise, Gopherus polyphemus, found in sandy habitats across the southeastern United States. We aimed to understand the overall bacterial community associated with A. tuberculatum while also focusing on spotted fever group Rickettsia. These tortoises in the Southern Mississippi region are a federally threatened species; therefore, we have carefully trapped the tortoises and removed the species-specific ticks attached to them. Genomic DNA was extracted from individual ticks and used to explore overall bacterial load using pyrosequencing of bacterial 16S rRNA on 454-sequencing platform. The spotted fever group of Rickettsia was explored by amplifying rickettsial outer membrane protein A (rompA) gene by nested PCR. Sequencing results revealed 330 bacterial operational taxonomic units (OTUs) after all the necessary curation of sequences. Four whole A. tuberculatum ticks showed Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes as the most dominant phyla with a total of 74 different bacterial genera detected. Together Rickettsiae and Francisella showed >85% abundance, thus dominating the bacterial community structure. Partial sequences obtained from ompA amplicons revealed the presence of an uncharacterized Rickettsia similar to the Rickettsial endosymbiont of A. tuberculatum. This is the first preliminary profile of a complete bacterial community from gopher tortoise ticks and warrants further investigation regarding the functional role of Rickettsial and Francisella-like endosymbionts in tick physiology.
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Affiliation(s)
- Khemraj Budachetri
- Department of Biological Sciences, University of Southern Mississippi, 118 College Drive #5018, Hattiesburg, MS 39406, USA
| | - Daniel Gaillard
- Department of Biological Sciences, University of Southern Mississippi, 118 College Drive #5018, Hattiesburg, MS 39406, USA
| | - Jaclyn Williams
- Department of Biological Sciences, University of Southern Mississippi, 118 College Drive #5018, Hattiesburg, MS 39406, USA
| | - Nabanita Mukherjee
- Department of Biological Sciences, University of Southern Mississippi, 118 College Drive #5018, Hattiesburg, MS 39406, USA
| | - Shahid Karim
- Department of Biological Sciences, University of Southern Mississippi, 118 College Drive #5018, Hattiesburg, MS 39406, USA.
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Intestinal Flora Modification of Arthritis Pattern in Spondyloarthropathy. J Clin Rheumatol 2016; 21:296-9. [PMID: 26267718 DOI: 10.1097/rhu.0000000000000279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
BACKGROUND The reactive form of spondyloarthropathy appears inducible by exposure to agents of infectious diarrhea, but do those organisms represent the tip of the iceberg, as indicated by renewed interest in gastrointestinal flora? Prevalence of spondyloarthropathy (20% of chimpanzees [Pan] and 28% of gorillas) is independent of subspecies and species, respectively. However, there are major differences in arthritis patterns, a characteristic shared with humans. OBJECTIVES Do patterns of arthritis correlate with gastrointestinal flora? Could such associated modifications be in the form of disease induction or represent protective effectors (at least against the extent of peripheral arthritis)? METHODS The skeletons of 2 chimpanzee subspecies (79 Pan troglodytes troglodytes and 26 Pan troglodytes schweinfurthii) and 2 gorilla species (99 Gorilla gorilla and 38 Gorilla beringei) adults were examined, and arthritis pattern noted. Feces of Eastern (P. schweinfurthii and G. beringei) and Western (great apes collected in their normal ranges) apes were assessed for 16S rRNA c and its character. RESULTS Patterns of arthritis recognized on examination of skeletons showed geographic variation in skeletal distribution. East African apes (P. troglodytes schweinfurthii and G. beringei) had pauciarticular arthritis and frequent sacroiliac disease, whereas West African apes (P. troglodytes troglodytes and G. gorilla) had polyarticular peripheral joint disease with minimal sacroiliac involvement. DNA evidence revealed that Corynebactericeae were prominently represented in great apes with polyarticular disease, whereas Dietzia and Bifidobacterium exposure correlated with reduced peripheral joint arthritis distribution. CONCLUSIONS Suggestions of a protective effect (in this case, limiting extent of peripheral arthritis, but not the disease itself) offered by these organisms are well represented by documented effects in other diseases (eg, tuberculosis) in the zoologic record. Perhaps it is this disease-modifying character that reduces the extent of the peripheral erosive disease, while increasing propensity to axial (sacroiliac) disease. A potential role for probiotic organisms in management of arthritis in humans is suggested, as has been documented for tuberculosis, gastrointestinal disorders, and food allergies.
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