1
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Zheng W, Liu J, Bai H, Xu X, Wu L, Qin X. A Patient of Spontaneous Bacterial Peritonitis in Hepatitis C Cirrhosis Caused by Gordonia terrae: A Case Report. Infect Drug Resist 2024; 17:1803-1810. [PMID: 38741944 PMCID: PMC11090189 DOI: 10.2147/idr.s459821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/25/2024] [Indexed: 05/16/2024] Open
Abstract
Background Gordonia terrae is an opportunistic pathogen that rarely causes clinical infections. Here, we first report a case of spontaneous bacterial peritonitis in patients with hepatitis C cirrhosis caused by Gordonia terrea. Case Presentation A 71-year-old male patient was diagnosed with spontaneous bacteria peritonitis secondary to hepatitis C cirrhosis. The result of bacterial culture in ascites was positive, and the pathogenic bacteria was preliminarily identified as the Gordonia genus by matrix-assisted laser desorption ionization-time of flight mass spectrometry. After 16S rRNA sequencing analysis, it was determined to be the Gordonia terrea. Symptoms relieved after treatment with ceftazidime. Conclusion This case indicates that the clinical infections caused by Gordonia terrea should be brought to the forefront. Accurate and rapid bacterial identification results are highly beneficial to the diagnosis and therapeutic regime.
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Affiliation(s)
- Wei Zheng
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Liaoning Clinical Research Center for Laboratory Medicine, Shengyang, People’s Republic of China
| | - Jianhua Liu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Liaoning Clinical Research Center for Laboratory Medicine, Shengyang, People’s Republic of China
| | - Haixia Bai
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Liaoning Clinical Research Center for Laboratory Medicine, Shengyang, People’s Republic of China
| | - Xin Xu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Liaoning Clinical Research Center for Laboratory Medicine, Shengyang, People’s Republic of China
| | - Lina Wu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Liaoning Clinical Research Center for Laboratory Medicine, Shengyang, People’s Republic of China
| | - Xiaosong Qin
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Liaoning Clinical Research Center for Laboratory Medicine, Shengyang, People’s Republic of China
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2
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Suphannarot A, Butdee W, Suriyachadkun C, Duangmal K, Mingma R. Gordonia prachuapensis sp. nov. and Gordonia sesuvii sp. nov., two novel actinobacteria isolated from mangrove sediments and leaves of halophyte Sesuvium portulacastrum in Thailand. Int J Syst Evol Microbiol 2024; 74. [PMID: 38805028 DOI: 10.1099/ijsem.0.006401] [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: 05/29/2024] Open
Abstract
A polyphasic approach was used to characterize two novel actinobacterial strains, designated PKS22-38T and LSe1-13T, which were isolated from mangrove soils and leaves of halophyte Sesuvium portulacastrum (L.), respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that they belonged to the genus Gordonia and were most closely related to three validly published species with similarities ranging from 98.6 to 98.1 %. The genomic DNA G+C contents of strains PKS22-38T and LSe1-13T were 67.3 and 67.2 mol%, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 93.3 and 54.9 %, respectively, revealing that they are independent species. Meanwhile, the ANI and dDDH values between the two novel strains and closely related type strains were below 80.5 and 24.0 %, respectively. Strains PKS22-38T and LSe1-13T contained C16 : 0, C18 : 1 ω9c and C18 : 0 10-methyl (TBSA) as the major fatty acids and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as the main phospholipids. The predominant menaquinone was MK-9(H2). Based on phenotypic, chemotaxonomic, phylogenetic and genomic data, strains PKS22-38T and LSe1-13T are considered to represent two novel species within the genus Gordonia, for which the names Gordonia prachuapensis sp. nov. and Gordonia sesuvii sp. nov. are proposed, with strain PKS22-38T (=TBRC 17540T=NBRC 116256T) and strain LSe1-13T (=TBRC 17706T=NBRC 116396T) as the type strains, respectively.
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Affiliation(s)
- Aekasit Suphannarot
- Division of Microbiology, Department of Science and Bioinnovation, Faculty of Liberal Arts and Science, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
| | - Waranya Butdee
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Chanwit Suriyachadkun
- BIOTEC Culture Collection, Biodiversity and Biotechnological Resource Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, Thailand
| | - Kannika Duangmal
- Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Ratchanee Mingma
- Division of Microbiology, Department of Science and Bioinnovation, Faculty of Liberal Arts and Science, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
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3
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Baumgartner BM, Bono KA, McIntosh DR, Vu AM, Adams CF, Benik BC, Chavez J, Gresky SJ, Sotelo A, Ray JI, Peister A, Kimberley KW, McKenna CC, Theoret JR, Yoon EJ, Windsor EJ. Genome sequences of actinobacteriophages JorRay, Blocker23, Nibbles, and OlgasClover. Microbiol Resour Announc 2024; 13:e0125623. [PMID: 38445868 PMCID: PMC11008117 DOI: 10.1128/mra.01256-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/26/2024] [Indexed: 03/07/2024] Open
Abstract
JorRay, Blocker23, Nibbles, and OlgasClover are actinobacteriophages belonging to clusters G1, B2, CT, and DJ, respectively. JorRay and Blocker23 were identified in host bacterium Mycobacterium smegmatis mc2155. Nibbles and OlgasClover were identified in host bacterium Gordonia rubripertincta NRRL B-16540.
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Affiliation(s)
| | - Kayla A. Bono
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Dawn R. McIntosh
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Anna M. Vu
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Chanel F. Adams
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Brooklyn C. Benik
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Jessica Chavez
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Samantha J. Gresky
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Andres Sotelo
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Jordan I. Ray
- Department of Biology, Morehouse College, Atlanta, Georgia, USA
| | | | - Kendra W. Kimberley
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Chelsey C. McKenna
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - James R. Theoret
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Earl J. Yoon
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Erin J. Windsor
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
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4
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Rhenals-Montoya P, Villamil L, Sánchez-Suárez J, Díaz L, Coy-Barrera E. Optimized carotenoid production and antioxidant capacity of Gordonia hongkongensis. Sci Prog 2024; 107:368504241253695. [PMID: 38801654 PMCID: PMC11135077 DOI: 10.1177/00368504241253695] [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] [Indexed: 05/29/2024]
Abstract
The current emphasis within the cosmetic market on sustainable ingredients has heightened the exploration of new sources for natural, active components. Actinomycetota, recognized for producing pigments with bioactive potential, offer promising functional cosmetic ingredients. This study aimed to optimize pigment and antioxidant metabolite production from the Gordonia hongkongensis strain EUFUS-Z928 by implementing the Plackett-Burman experimental design and response surface methodology. Extracts derived from this strain exhibited no cytotoxic activity against human primary dermal fibroblast (HDFa, ATCC® PCS-201-012™, Primary Dermal Fibroblast; Normal, Human, Adult). Eight variables, including inoculum concentration, carbon and nitrogen source concentration, NaCl concentration, pH, incubation time, temperature, and stirring speed, were analyzed using the Plackett-Burman experimental design. Subsequently, factors significantly influencing pigment and antioxidant metabolite production, such as temperature, inoculum concentration, and agitation speed, were further optimized using response surface methodology and Box-Behnken design. The results demonstrated a substantial increase in absorbance (from 0.091 to 0.32), DPPH radical scavenging capacity (from 27.60% to 84.61%), and ABTS radical scavenging capacity (from 17.39% to 79.77%) compared to responses obtained in the isolation medium. The validation of the mathematical model accuracy exceeded 90% for all cases. Furthermore, liquid chromatography coupled with mass spectrometry (LC-MS) facilitated the identification of compounds potentially responsible for enhanced pigment production and antioxidant capacity in extracts derived from G. hongkongensis. Specifically, six carotenoids, red-orange pigments with inherent antioxidant capacity, were identified as the main enhanced compounds. This comprehensive approach effectively optimized the culture conditions and medium of a G. hongkongensis strain, resulting in enhanced carotenoid production and antioxidant capacity. Beyond identifying bioactive compounds and their potential cosmetic applications, this study offers insights into the broader industrial applicability of these extracts. It underscores the potential of G. hongkongensis and hints at the future utilization of other untapped sources of rare actinomycetes within the industry.
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Affiliation(s)
- Paula Rhenals-Montoya
- Master in Process Design and Management, School of Engineering, Universidad de La Sabana, Chia, Colombia
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chia, Colombia
| | - Luisa Villamil
- Agroindustrial Production Research Group, Doctorate of Biosciences, School of Engineering, Universidad de La Sabana, Chia, Colombia
| | - Jeysson Sánchez-Suárez
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chia, Colombia
| | - Luis Díaz
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chia, Colombia
- Agroindustrial Production Research Group, Doctorate of Biosciences, School of Engineering, Universidad de La Sabana, Chia, Colombia
| | - Ericsson Coy-Barrera
- Bioorganic Chemistry Laboratory, Universidad Militar Nueva Granada, Cajicá, Colombia
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5
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Wang H, Guan F, Zhu Y, Pan Y, Liu Q, Liu Q, He W, Gong D, Tian J, Han D. Biofilm formation promoted biodegradation of polyethylene in Gordonia polyisoprenivorans B251 isolated from bacterial enrichment acclimated by hexadecane for two years. CHEMOSPHERE 2023; 344:140383. [PMID: 37832891 DOI: 10.1016/j.chemosphere.2023.140383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 08/31/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
Polyethylene (PE) mulch films have been widely used in agriculture and led to a significant pollution in cultivated soils. It is desirable to develop the sustainable method for the degradation of PE. As an environment friendly approach, microbial or enzymatic degradation of PE could meet this demanding. Thus, more microbial strains are required for illustrating biodegrading pathway and developing efficient biological method. In this study, Gordonia polyisoprenivorans B251 capable of degrading PE was isolated from bacterial enrichment with hexadecane as a sole carbon source for two years, in which genus Gordonia had dominated. As revealed by microbial growth curve, the strain B251 had the highest growth rate than other tested strains in the mediums either with hexadecane or PE particles as sole carbon source. The formation of biofilms in both enriched culture and G. polyisoprenivorans B251 pure culture attached to PE film was observed. The capability for PE degradation of individual strain was screened by 30-day incubation with PE film and confirmed by the presence of hydroxyl, carbonyl, carbon-carbon double bond and ether groups in FT-IR analysis and cracks on the surface of PE film observed by scanning electron microscopy (SEM). Therefore, Gordonia polyisoprenivorans, reported as their degradation of environmental contaminants in previous study, were also identified in current study as a candidate for polyethylene biodegradation.
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Affiliation(s)
- Hongzhe Wang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of the Chinese Academy of Sciences, Beijing, 100049, China; Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Feifei Guan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yan Zhu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Yanshuo Pan
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China; Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qi Liu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qin Liu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wenqing He
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Daozhi Gong
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jian Tian
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Dongfei Han
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China.
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6
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Grimm D, Guy N, Lengyel G, Franks J, Maltman C. Gordonia metallireducens sp. nov., a tellurite- and selenite-resistant bacterium isolated from the sediment of an acid mine drainage stream. Int J Syst Evol Microbiol 2023; 73. [PMID: 37990983 DOI: 10.1099/ijsem.0.006176] [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: 11/23/2023] Open
Abstract
A polyphasic taxonomic study was carried out on strain TSed Te1T, isolated from sediment of a stream contaminated with acid drainage from a coal mine. The bacterium forms pink-pigmented colonies and has a rod-coccus growth cycle, which also includes some coryneform arrangements. This bacterium is capable of growing in the presence of up to 750 μg ml-1 tellurite and 5000 μg ml-1 selenite, reducing each to elemental form. Nearly complete 16S rRNA gene sequence analysis associated the strain with Gordonia, with 99.5 and 99.3 % similarity to Gordonia namibiensis and Gordonia rubripertincta, respectively. Computation of the average nucleotide identity and digital DNA-DNA hybridization comparisons with the closest phylogenetic neighbour of TSed Te1T revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The dominant fatty acids were C16 : 0, C18 : 1, C16 : 1 and tuberculostearic acid. The DNA G+C content was 67.6 mol%. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside, while MK-9(H2) was the only menaquinone found. Mycolic acids of C56-C60 were present. Whole-cell hydrolysates contained meso-diaminopimelic acid along with arabinose and galactose as the major cell-wall sugars. On the basis of the results obtained in this study, the bacterium was assigned to the genus Gordonia and represents a new species with the name Gordonia metallireducens sp. nov. The type strain is TSed Te1T (=NRRL B-65678T=DSM 114093T).
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Affiliation(s)
- David Grimm
- Department of Microbiology, Miami University College of Arts and Science, Oxford, Ohio 45056, USA
| | - Nathan Guy
- Department of Chemistry, Slippery Rock University, Slippery Rock, Pennsylvania, USA
| | - George Lengyel
- Department of Chemistry, Slippery Rock University, Slippery Rock, Pennsylvania, USA
| | - Jonathan Franks
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
| | - Chris Maltman
- Department of Biology, Slippery Rock University, Slippery Rock, Pennsylvania 16057, USA
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7
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Meng B, Bleau A, Bombaywala RR, DeGraw AS, Deol MS, Dollard KE, Gentile N, Jebaraj J, Kayayan GN, Miranda BC, Momoh AE, Morales E, Nunes AC, Oropallo AM, Otterstedt SC, Pridell AT, Roberts JI, Ruiz GA, Sangasani D, Smith RD, Tarar M, Singh V, Jayachandran P. Complete genome sequences of G ordonia rubripertincta phages OtterstedtS21 and Patos. Microbiol Resour Announc 2023; 12:e0071823. [PMID: 37772859 PMCID: PMC10586170 DOI: 10.1128/mra.00718-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 08/24/2023] [Indexed: 09/30/2023] Open
Abstract
We report the genomes of two viruses with siphovirus morphology, OtterstedtS21 and Patos, from Albany, New York, using Gordonia rubripertincta. The genomes of OtterstedtS21 and Patos are ~68 kbp long with 58% GC content. Both phages group with cluster DV based on gene content similarity to phages in the Actinobacteriophage database.
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Affiliation(s)
- Bowen Meng
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Alexander Bleau
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Riddhi R. Bombaywala
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Audrey S. DeGraw
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Manjot S. Deol
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Kendall E. Dollard
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Nicolas Gentile
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Julianna Jebaraj
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Gregory N. Kayayan
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Briana C. Miranda
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Ayobamidele E. Momoh
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Elias Morales
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Amalia C. Nunes
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Antonia M. Oropallo
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Sophia C. Otterstedt
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Anna T. Pridell
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Jenna I. Roberts
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Gabriel A. Ruiz
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Dhatri Sangasani
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Renee D. Smith
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Mahad Tarar
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Vir Singh
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Pradeepa Jayachandran
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
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8
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De Filippis F, Bonelli M, Bruno D, Sequino G, Montali A, Reguzzoni M, Pasolli E, Savy D, Cangemi S, Cozzolino V, Tettamanti G, Ercolini D, Casartelli M, Caccia S. Plastics shape the black soldier fly larvae gut microbiome and select for biodegrading functions. MICROBIOME 2023; 11:205. [PMID: 37705113 PMCID: PMC10500907 DOI: 10.1186/s40168-023-01649-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 07/16/2023] [Indexed: 09/15/2023]
Abstract
BACKGROUND In the last few years, considerable attention has been focused on the plastic-degrading capability of insects and their gut microbiota in order to develop novel, effective, and green strategies for plastic waste management. Although many analyses based on 16S rRNA gene sequencing are available, an in-depth analysis of the insect gut microbiome to identify genes with plastic-degrading potential is still lacking. RESULTS In the present work, we aim to fill this gap using Black Soldier Fly (BSF) as insect model. BSF larvae have proven capability to efficiently bioconvert a wide variety of organic wastes but, surprisingly, have never been considered for plastic degradation. BSF larvae were reared on two widely used plastic polymers and shotgun metagenomics was exploited to evaluate if and how plastic-containing diets affect composition and functions of the gut microbial community. The high-definition picture of the BSF gut microbiome gave access for the first time to the genomes of culturable and unculturable microorganisms in the gut of insects reared on plastics and revealed that (i) plastics significantly shaped bacterial composition at species and strain level, and (ii) functions that trigger the degradation of the polymer chains, i.e., DyP-type peroxidases, multicopper oxidases, and alkane monooxygenases, were highly enriched in the metagenomes upon exposure to plastics, consistently with the evidences obtained by scanning electron microscopy and 1H nuclear magnetic resonance analyses on plastics. CONCLUSIONS In addition to highlighting that the astonishing plasticity of the microbiota composition of BSF larvae is associated with functional shifts in the insect microbiome, the present work sets the stage for exploiting BSF larvae as "bioincubators" to isolate microbial strains and enzymes for the development of innovative plastic biodegradation strategies. However, most importantly, the larvae constitute a source of enzymes to be evolved and valorized by pioneering synthetic biology approaches. Video Abstract.
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Affiliation(s)
- Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Marco Bonelli
- Department of Biosciences, University of Milan, Milan, Italy
| | - Daniele Bruno
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Giuseppina Sequino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Aurora Montali
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Marcella Reguzzoni
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Davide Savy
- Interdepartmental Research Centre of Nuclear Magnetic Resonance for the Environment, Agri-Food and New Materials (CERMANU), University of Naples Federico II, Portici, Italy
| | - Silvana Cangemi
- Interdepartmental Research Centre of Nuclear Magnetic Resonance for the Environment, Agri-Food and New Materials (CERMANU), University of Naples Federico II, Portici, Italy
| | - Vincenza Cozzolino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Interdepartmental Research Centre of Nuclear Magnetic Resonance for the Environment, Agri-Food and New Materials (CERMANU), University of Naples Federico II, Portici, Italy
| | - Gianluca Tettamanti
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Portici, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy.
| | - Morena Casartelli
- Department of Biosciences, University of Milan, Milan, Italy.
- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Portici, Italy.
| | - Silvia Caccia
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy.
- Department of Biosciences, University of Milan, Milan, Italy.
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9
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Vergov B, Angelova A, Baldzhieva A, Kalchev Y, Tsochev G, Murdjeva M. Gordonia sputi as an Arising Causative Agent of Bacteremia in Immunocompromised Comorbid Dialysis Patients-A Case Report. Healthcare (Basel) 2023; 11:2059. [PMID: 37510501 PMCID: PMC10379339 DOI: 10.3390/healthcare11142059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Improvements in medical care have turned severe diseases into chronic conditions, but often their treatment and the use of medical devices are related to specific complications. Here, we present a clinical case of a long-term dialysis patient who was infected with a rare opportunistic infectious agent-Gordonia sputi. In recent years, the incidence of Gordonia spp. infections in immunocompromised patients with central venous catheters (CVC) has appeared to rise. The isolation and identification of Gordonia spp. are challenging and require modern techniques. In addition, the treatment is usually persistent and often results in CVC extraction, which is associated with further risk and costs for the patient. We also studied the alterations in the immune status of the patient caused by long-term renal replacement therapy and persistent hepatitis C virus infection. Antibiotic therapy and immunostimulation with Inosine pranobex lead to successful eradication of the infection without the need for CVC replacement.
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Affiliation(s)
- Bozhidar Vergov
- Department of Medical Biology, Faculty of Medicine, Medical University of Plovdiv, 4000 Plovdiv, Bulgaria
- Department of Dialysis Treatment, St George University Hospital, 6000 Plovdiv, Bulgaria
| | - Andreana Angelova
- Department of Medical Microbiology and Immunology "Prof. Dr. Elissay Yanev", Faculty of Pharmacy, Medical University of Plovdiv, 4000 Plovdiv, Bulgaria
- Laboratory of Microbiology, St George University Hospital, 6000 Plovdiv, Bulgaria
- Research Institute at Medical University of Plovdiv, 4000 Plovdiv, Bulgaria
| | - Alexandra Baldzhieva
- Department of Medical Microbiology and Immunology "Prof. Dr. Elissay Yanev", Faculty of Pharmacy, Medical University of Plovdiv, 4000 Plovdiv, Bulgaria
- Research Institute at Medical University of Plovdiv, 4000 Plovdiv, Bulgaria
- Laboratory of Clinical Immunology, St George University Hospital, 6000 Plovdiv, Bulgaria
| | - Yordan Kalchev
- Department of Medical Microbiology and Immunology "Prof. Dr. Elissay Yanev", Faculty of Pharmacy, Medical University of Plovdiv, 4000 Plovdiv, Bulgaria
- Laboratory of Microbiology, St George University Hospital, 6000 Plovdiv, Bulgaria
- Research Institute at Medical University of Plovdiv, 4000 Plovdiv, Bulgaria
| | - Georgi Tsochev
- Department of Dialysis Treatment, St George University Hospital, 6000 Plovdiv, Bulgaria
| | - Marianna Murdjeva
- Department of Medical Microbiology and Immunology "Prof. Dr. Elissay Yanev", Faculty of Pharmacy, Medical University of Plovdiv, 4000 Plovdiv, Bulgaria
- Laboratory of Microbiology, St George University Hospital, 6000 Plovdiv, Bulgaria
- Research Institute at Medical University of Plovdiv, 4000 Plovdiv, Bulgaria
- Laboratory of Clinical Immunology, St George University Hospital, 6000 Plovdiv, Bulgaria
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10
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Rellegadla S, Prajapat G, Jain S, Agrawal A. Microbial communities succession post to polymer flood demonstrate a role in enhanced oil recovery. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12673-3. [PMID: 37428189 DOI: 10.1007/s00253-023-12673-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 04/03/2023] [Accepted: 06/15/2023] [Indexed: 07/11/2023]
Abstract
The role of indigenous microbial communities in residual oil extraction following a recovery process is not well understood. This study investigated the dynamics of resident microbial communities in oil-field simulating sand pack bioreactors after the polymer flooding stage resumed with waterflooding and explored their contribution to the oil extraction process. The microbial community succession was studied through high-throughput sequencing of 16S rRNA genes. The results revealed alternating dominance of minority populations, including Dietzia sps., Acinetobacter sps., Soehngenia sps., and Paracoccus sps., in each bioreactor following the flooding process. Additionally, the post-polymer waterflooding stage led to higher oil recovery, with hydroxyethylcellulose, tragacanth gum, and partially hydrolyzed polyacrylamide polymer-treated bioreactors yielding additional recovery of 4.36%, 5.39%, and 3.90% residual oil in place, respectively. The dominant microbial communities were previously reported to synthesize biosurfactants and emulsifiers, as well as degrade and utilize hydrocarbons, indicating their role in aiding the recovery process. However, the correlation analysis of the most abundant taxa showed that some species were more positively correlated with the oil recovery process, while others acted as competitors for the carbon source. The study also found that higher biomass favored the plugging of high permeability zones in the reservoir, facilitating the dislodging of crude oil in new channels. In conclusion, this study suggests that microbial populations significantly shift upon polymer treatment and contribute synergistically to the oil recovery process depending on the characteristics of the polymers injected. KEY POINTS: • Post-polymer flooded microbial ecology shows unique indigenous microbial consortia. • Injected polymers are observed to act as enrichment substrates by resident communities. • The first study to show successive oil recovery stage post-polymer flood without external influence.
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Affiliation(s)
- Sandeep Rellegadla
- Energy and Environment Research Laboratory, Department of Microbiology, Central University of Rajasthan, NH-8, Bandersindri, Kishangarh, Ajmer, Rajasthan, 305817, India
- Centre for Water Technology, Department of Biological and Chemical Engineering, Aarhus University, Universitetsbyen 36, 8000, Aarhus C, Denmark
| | - Ganshyam Prajapat
- The Energy and Resources Institute (TERI), Darbari Seth Block, India Habitat Centre, Lodhi Road, New Delhi, 110003, India
| | - Shikha Jain
- Enercosm Pvt. Ltd., Jaipur, Rajasthan, 302019, India
| | - Akhil Agrawal
- Energy and Environment Research Laboratory, Department of Microbiology, Central University of Rajasthan, NH-8, Bandersindri, Kishangarh, Ajmer, Rajasthan, 305817, India.
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11
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Behera S, Das S. Potential and prospects of Actinobacteria in the bioremediation of environmental pollutants: Cellular mechanisms and genetic regulations. Microbiol Res 2023; 273:127399. [PMID: 37150049 DOI: 10.1016/j.micres.2023.127399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/22/2023] [Accepted: 04/30/2023] [Indexed: 05/09/2023]
Abstract
Increasing industrialization and anthropogenic activities have resulted in the release of a wide variety of pollutants into the environment including pesticides, polycyclic aromatic hydrocarbons (PAHs), and heavy metals. These pollutants pose a serious threat to human health as well as to the ecosystem. Thus, the removal of these compounds from the environment is highly important. Mitigation of the environmental pollution caused by these pollutants via bioremediation has become a promising approach nowadays. Actinobacteria are a group of eubacteria mostly known for their ability to produce secondary metabolites. The morphological features such as spore formation, filamentous growth, higher surface area to volume ratio, and cellular mechanisms like EPS secretion, and siderophore production in Actinobacteria render higher resistance and biodegradation ability. In addition, these bacteria possess several oxidoreductase systems (oxyR, catR, furA, etc.) which help in bioremediation. Actinobacteria genera including Arthrobacter, Rhodococcus, Streptomyces, Nocardia, Microbacterium, etc. have shown great potential for the bioremediation of various pollutants. In this review, the bioremediation ability of these bacteria has been discussed in detail. The utilization of various genera of Actinobacteria for the biodegradation of organic pollutants, including pesticides and PAHs, and inorganic pollutants like heavy metals has been described. In addition, the cellular mechanisms in these microbes which help to withstand oxidative stress have been discussed. Finally, this review explores the Actinobacteria mediated strategies and recent technologies such as the utilization of mixed cultures, cell immobilization, plant-microbe interaction, utilization of biosurfactants and nanoparticles, etc., to enhance the bioremediation of various environmental pollutants.
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Affiliation(s)
- Shivananda Behera
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India.
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12
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Barthel A, Ursenbach A, Kaeuffer C, Koebel C, Gravet A, De Briel D, Dubois J, Haerrel E, Rougier E, Gerber V. Characteristics and Treatment of Gordonia spp. Bacteremia, France. Emerg Infect Dis 2023; 29:1025-1028. [PMID: 37081585 PMCID: PMC10124657 DOI: 10.3201/eid2905.221901] [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: 04/22/2023] Open
Abstract
Systemic Gordonia spp. infections are rare and occur mostly among immunocompromised patients. We analyzed 10 cases of Gordonia bacteremia diagnosed in 3 tertiary care centers in France to assess risk factors, treatment, and clinical outcomes. Most patients were cured within 10 days by using β-lactam antimicrobial therapy and removing central catheters.
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13
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A Unique Case of Gordonia bronchialis Pneumonia. Arch Bronconeumol 2023; 59:114-115. [PMID: 36437181 DOI: 10.1016/j.arbres.2022.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/08/2022]
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14
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Trejo A, Masdeu C, Serrano-Pérez I, Pedrola M, Juanola N, Ghashghaei O, Jiménez-Galisteo G, Lavilla R, Palacios F, Alonso C, Viñas M. Efficient AntiMycolata Agents by Increasing the Lipophilicity of Known Antibiotics through Multicomponent Reactions. Antibiotics (Basel) 2023; 12:antibiotics12010083. [PMID: 36671284 PMCID: PMC9854905 DOI: 10.3390/antibiotics12010083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
New antibiotic agents were prepared using Povarov and Ugi multicomponent reactions upon the known drugs sulfadoxine and dapsone. The prepared derivatives, with increased lipophilicity, showed improved efficiency against Mycolata bacteria. Microbiological guidance for medicinal chemistry is a powerful tool to design new and effective antimicrobials. In this case, the readily synthesized compounds open new possibilities in the search for antimicrobials active on mycolic acid-containing bacteria.
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Affiliation(s)
- Angela Trejo
- Departamento de Química Orgánica I, Facultad de Farmacia, Universidad del País Vasco/Euskal Herriko, Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Carme Masdeu
- Departamento de Química Orgánica I, Facultad de Farmacia, Universidad del País Vasco/Euskal Herriko, Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Irene Serrano-Pérez
- Laboratory of Molecular Microbiology & Antimicrobials, Department of Pathology & Experimental Therapeutics, Medical School, University of Barcelona and IDIBELL, Feixa Llarga, s/n, 08907 Hospitalet de Llobregat, Spain
| | - Marina Pedrola
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB), University of Barcelona, Av. de Joan XXIII, 27-31, 08028 Barcelona, Spain
| | - Narcís Juanola
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB), University of Barcelona, Av. de Joan XXIII, 27-31, 08028 Barcelona, Spain
| | - Ouldouz Ghashghaei
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB), University of Barcelona, Av. de Joan XXIII, 27-31, 08028 Barcelona, Spain
| | - Guadalupe Jiménez-Galisteo
- Laboratory of Molecular Microbiology & Antimicrobials, Department of Pathology & Experimental Therapeutics, Medical School, University of Barcelona and IDIBELL, Feixa Llarga, s/n, 08907 Hospitalet de Llobregat, Spain
| | - Rodolfo Lavilla
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB), University of Barcelona, Av. de Joan XXIII, 27-31, 08028 Barcelona, Spain
- Correspondence: (R.L.); (C.A.); (M.V.)
| | - Francisco Palacios
- Departamento de Química Orgánica I, Facultad de Farmacia, Universidad del País Vasco/Euskal Herriko, Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Concepción Alonso
- Departamento de Química Orgánica I, Facultad de Farmacia, Universidad del País Vasco/Euskal Herriko, Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
- Correspondence: (R.L.); (C.A.); (M.V.)
| | - Miguel Viñas
- Laboratory of Molecular Microbiology & Antimicrobials, Department of Pathology & Experimental Therapeutics, Medical School, University of Barcelona and IDIBELL, Feixa Llarga, s/n, 08907 Hospitalet de Llobregat, Spain
- Correspondence: (R.L.); (C.A.); (M.V.)
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15
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Alnajjar M, Mudawi D, Cherif H, Hashim SM, Zaqout A, Bougaila A, Jibril FI, Mohamed SF. Central catheter-related Gordonia bronchialis bacteremia in an immunocompromised patient: A case report, and literature review. IDCases 2023; 32:e01738. [PMID: 36938335 PMCID: PMC10014288 DOI: 10.1016/j.idcr.2023.e01738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/04/2023] [Accepted: 03/05/2023] [Indexed: 03/08/2023] Open
Abstract
Gordonia is a rarely reported organism causing central line-associated bloodstream infection (CLABSI). This article reports an acute myeloid leukemia (AML) case in which the patient developed febrile neutropenia and was later found to have Gordonia bronchialis (G. bronchialis) CLABSI. The patient received a two-week ceftriaxone regimen, based on susceptibility. The microbiologic diagnosis of this organism is considered challenging due to its resemblance with other organisms; however, more sophisticated methods of diagnosis (such as gene sequencing) can aid in differentiation.
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Affiliation(s)
- Mohammed Alnajjar
- Division of Internal Medicine, Hamad Medical Corporation, Doha, Qatar
- Correspondence to: Division of Internal Medicine, Hamad Medical Corporation, 950 Al-Qawafel Street, Alsadd Area, Doha, Qatar.
| | - Deena Mudawi
- Division of Hematology, National Center for Cancer Care and Research (NCCCR), Doha, Qatar
| | - Honar Cherif
- Division of Hematology, National Center for Cancer Care and Research (NCCCR), Doha, Qatar
| | - Samar Mahmoud Hashim
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar
- Communicable Disease Center, Hamad Medical Corporation, Doha, Qatar
| | - Ahmed Zaqout
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar
- Communicable Disease Center, Hamad Medical Corporation, Doha, Qatar
| | - Amina Bougaila
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar
- Communicable Disease Center, Hamad Medical Corporation, Doha, Qatar
| | | | - Shehab Fareed Mohamed
- Division of Hematology, National Center for Cancer Care and Research (NCCCR), Doha, Qatar
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16
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Mhuireach GÁ, Fahimipour AK, Vandegrift R, Muscarella ME, Hickey R, Bateman AC, Van Den Wymelenberg KG, Bohannan BJM. Temporary establishment of bacteria from indoor plant leaves and soil on human skin. ENVIRONMENTAL MICROBIOME 2022; 17:61. [PMID: 36572917 PMCID: PMC9793532 DOI: 10.1186/s40793-022-00457-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Plants are found in a large percentage of indoor environments, yet the potential for bacteria associated with indoor plant leaves and soil to colonize human skin remains unclear. We report results of experiments in a controlled climate chamber to characterize bacterial communities inhabiting the substrates and leaves of five indoor plant species, and quantify microbial transfer dynamics and residence times on human skin following simulated touch contact events. Controlled bacterial propagule transfer events with soil and leaf donors were applied to the arms of human occupants and repeatedly measured over a 24-h period using 16S rRNA gene amplicon sequencing. RESULTS Substrate samples had greater biomass and alpha diversity compared to leaves and baseline skin bacterial communities, as well as dissimilar taxonomic compositions. Despite these differences in donor community diversity and biomass, we observed repeatable patterns in the dynamics of transfer events. Recipient human skin bacterial communities increased in alpha diversity and became more similar to donor communities, an effect which, for soil contact only, persisted for at least 24 h. Washing with soap and water effectively returned communities to their pre-perturbed state, although some abundant soil taxa resisted removal through washing. CONCLUSIONS This study represents an initial characterization of bacterial relationships between humans and indoor plants, which represent a potentially valuable element of biodiversity in the built environment. Although environmental microbiota are unlikely to permanently colonize skin following a single contact event, repeated or continuous exposures to indoor biodiversity may be increasingly relevant for the functioning and diversity of the human microbiome as urbanization continues.
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Affiliation(s)
- Gwynne Á Mhuireach
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, USA.
| | - Ashkaan K Fahimipour
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, USA
| | - Roo Vandegrift
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, USA
- United States Department of Agriculture, APHIS, PPQ, Miami, FL, USA
| | - Mario E Muscarella
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Roxana Hickey
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, USA
| | - Ashley C Bateman
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, USA
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17
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Frantsuzova E, Bogun A, Vetrova A, Delegan Y. Methods of Identifying Gordonia Strains in Clinical Samples. Pathogens 2022; 11:pathogens11121496. [PMID: 36558832 PMCID: PMC9786905 DOI: 10.3390/pathogens11121496] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Gordonia spp. are members of the family Gordoniacea in the suborder Corynebacteriales; their habitat, in most cases, is soil. Many representatives of this genus are human or veterinary pathogens. The main cause of the lack of a standardized approach to dealing with infections caused by Gordonia is their erroneous identification and little information regarding their susceptibility to antimicrobial drugs. This review presents the most common methods for identifying Gordonia strains, including modern approaches for identifying a species. The main prospects and future directions of this field of knowledge are briefly presented.
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Affiliation(s)
- Ekaterina Frantsuzova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
| | - Alexander Bogun
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russia
| | - Anna Vetrova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
| | - Yanina Delegan
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
- Correspondence:
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18
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He Y, Lyu L, Hu Z, Yu Z, Shao Z. Gordonia tangerina sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748478 DOI: 10.1099/ijsem.0.005632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A Gram-stain-positive, aerobic bacterium, designated GW1C4-4T, was isolated from the seawater sample from the tidal zone of Guanyinshan Coast, Xiamen, Fujian Province, PR China. The strain was reddish-orange, rod-shaped and non-motile. Cells of strain GW1C4-4T were oxidase-negative and catalase-positive. The strain could grow at 10-42 °C (optimum, 32-35 °C), pH 5-9 (optimum, pH 6) and with 0-10 % NaCl (w/v; optimum, 1 %). Phylogenetic analysis based on the 16S rRNA sequences indicated that strain GW1C4-4T belonged to the genus Gordonia, having the highest similarity to Gordonia mangrovi HNM0687T (98.5 %), followed by Gordonia bronchialis DSM 43247T (98.4 %). The G+C DNA content was 66.5 mol %. Average nucleotide identity and digital DNA-DNA hybridization values between strain GW1C4-4T and G. mangrovi HNM0687T were 85.8 and 30.0 %, respectively. The principal fatty acids of strain GW1C4-4T were C16 : 0, C18 : 0 10-methyl (TBSA) and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). MK-9 (H2) was the sole respiratory quinone. The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified lipid. Based on its phylogenetic, phenotypic, chemotaxonomic and genomic characteristics, it is proposed that strain GW1C4-4T represents a novel species within the genus Gordonia, for which the name Gordonia tangerina sp. nov. is proposed. The type strain is GW1C4-4T (=MCCC 1A18727T=KCTC 49729T).
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Affiliation(s)
- Yufei He
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China.,State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, PR China.,University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Lina Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, Guangdong, PR China
| | - Ziyan Hu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Zhiqiang Yu
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
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19
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Sánchez-Suárez J, Díaz L, Coy-Barrera E, Villamil L. Specialized Metabolism of Gordonia Genus: An Integrated Survey on Chemodiversity Combined with a Comparative Genomics-Based Analysis. BIOTECH (BASEL (SWITZERLAND)) 2022; 11:biotech11040053. [PMID: 36412754 PMCID: PMC9680422 DOI: 10.3390/biotech11040053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022]
Abstract
Members of the phylum Actinomycetota (formerly Actinobacteria) have historically been the most prolific providers of small bioactive molecules. Although the genus Streptomyces is the best-known member for this issue, other genera, such as Gordonia, have shown interesting potential in their specialized metabolism. Thus, we combined herein the result of a comprehensive literature survey on metabolites derived from Gordonia strains with a comparative genomic analysis to examine the potential of the specialized metabolism of the genus Gordonia. Thirty Gordonia-derived compounds of different classes were gathered (i.e., alkaloids, amides, phenylpropanoids, and terpenoids), exhibiting antimicrobial and cytotoxic activities, and several were also isolated from Streptomyces (e.g., actinomycin, nocardamin, diolmycin A1). With the genome data, we estimated an open pan-genome of 57,901 genes, most of them being part of the cloud genome. Regarding the BGCs content, 531 clusters were found, including Terpenes, RiPP-like, and NRPS clusters as the most frequent clusters. Our findings demonstrated that Gordonia is a poorly studied genus in terms of its specialized metabolism production and potential applications. Nevertheless, given their BGCs content, Gordonia spp. are a valuable biological resource that could expand the chemical spectrum of the phylum Actinomycetota, involving novel BGCs for inspiring innovative outlines for synthetic biology and further use in biotechnological initiatives. Therefore, further studies and more efforts should be made to explore different environments and evaluate other bioactivities.
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Affiliation(s)
- Jeysson Sánchez-Suárez
- Doctoral Program in Biosciences, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia
| | - Luis Díaz
- Doctoral Program in Biosciences, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia
| | - Ericsson Coy-Barrera
- Bioorganic Chemistry Laboratory, Universidad Militar Nueva Granada, Cajicá 250247, Colombia
| | - Luisa Villamil
- Doctoral Program in Biosciences, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia
- Correspondence:
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20
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Pollenz RS, Bland J, Pope WH. Bioinformatic characterization of endolysins and holin-like membrane proteins in the lysis cassette of phages that infect Gordonia rubripertincta. PLoS One 2022; 17:e0276603. [PMID: 36395171 PMCID: PMC9671378 DOI: 10.1371/journal.pone.0276603] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/11/2022] [Indexed: 11/19/2022] Open
Abstract
Holins are bacteriophage-encoded transmembrane proteins that function to control the timing of bacterial lysis event, assist with the destabilization of the membrane proton motive force and in some models, generate large "pores" in the cell membrane to allow the exit of the phage-encoded endolysin so they can access the peptidoglycan components of the cell wall. The lysis mechanism has been rigorously evaluated through biochemical and genetic studies in very few phages, and the results indicate that phages utilize endolysins, holins and accessory proteins to the outer membrane to achieve cell lysis through several distinct operational models. This observation suggests the possibility that phages may evolve novel variations of how the lysis proteins functionally interact in an effort to improve fitness or evade host defenses. To begin to address this hypothesis, the current study utilized a comprehensive bioinformatic approach to systematically identify the proteins encoded by the genes within the lysis cassettes in 16 genetically diverse phages that infect the Gram-positive Gordonia rubripertincta NRLL B-16540 strain. The results show that there is a high level of diversity of the various lysis genes and 16 different genome organizations of the putative lysis cassette, many which have never been described. Thirty-four different genes encoding holin-like proteins were identified as well as a potential holin-major capsid fusion protein. The holin-like proteins contained between 1-4 transmembrane helices, were not shared to a high degree amongst the different phages and are present in the lysis cassette in a wide range of combinations of up to 4 genes in which none are duplicated. Detailed evaluation of the transmembrane domains and predicted membrane topologies of the holin-like proteins show that many have novel structures that have not been previously characterized. These results provide compelling support that there are novel operational lysis models yet to be discovered.
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Affiliation(s)
- Richard S. Pollenz
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, United States of America
| | - Jackson Bland
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, United States of America
| | - Welkin H. Pope
- Science Department, Chatham University, Pittsburgh, Pennsylvania, United States of America
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21
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Land-use change alters the bacterial community structure, but not forest management. Folia Microbiol (Praha) 2022; 68:277-290. [PMID: 36273059 DOI: 10.1007/s12223-022-01009-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 10/04/2022] [Indexed: 11/04/2022]
Abstract
Deforestation has a large impact on soil fertility, especially on steep slopes, but by applying sustainable management practices, local communities in Oaxaca (Mexico) have tried to avoid the most negative effects on the forest ecosystems they manage. In this study, the characteristics and bacterial community structure were investigated from soil sampled in triplicate (n = 3) with different land use, i.e., arable, natural forest, sustainable managed, and reforested soil. The pH was significantly higher in the arable (6.2) than in the forest soils (≤ 5.3), while the organic matter was > 2 times higher in the natural forest (80.4 g/kg) and sustainable managed soil (86.3 g/kg) than in the arable (36.8 g/kg) and cleared and reforested soil (39.3 g/kg). The higher organic matter content in the first two soils was due to leaf litter, absent in the other soils. The species richness (q = 0), the typical (q = 1) and dominant bacteria (q = 2) were not affected significantly by land use. The beta diversity, however, showed a significant effect of land use on species richness (p = 0.0029). Proteobacteria (40.135%) and Actinobacteria (20.15%) were the dominant bacterial phyla, and Halomonas (14.50%) and the Verrucomicrobia DA101 (3.39%) were the dominant genera. The bacterial communities were highly significantly different in soil with different land use considering the taxonomic level of genus and OTUs (p ≤ 0.003). It was found that the sustainable managed forest provided the local community with sellable wood while maintaining the soil organic matter content, i.e., sequestered C and without altering the bacterial community structure.
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22
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Huang Y, Gong J, Dong L, Yang J, Lu S, Lai XH, Pu J, Jin D, Xu J. Gordonia zhenghanii sp. nov. and Gordonia liuliyuniae sp. nov., isolated from bat faeces. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
Four mesophilic actinobacteria (HY002T, HY442, HY366T and HY285) isolated from the faeces of bats collected in southern China were found to be strictly aerobic, non-motile, rod-shaped, oxidase-negative, Gram-stain-positive and catalase-positive. Strains HY002T and HY366T contained meso-diaminopimelic acid as the diagnostic diamino acid and MK-9(H2) the sole respiratory quinone. Arabinose, galactose and ribose were detected in the whole-cell hydrolysates of both type strains. The main cellular fatty acids (> 10.0%) of all strains were C16 : 0, C18 : 1
ω9c, 10-methyl-C18 : 0 and summed feature 3. Strains HY002T and HY366T contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidyl inositol mannosides as the major polar lipids. The phylogenetic/phylogenomic analyses based on 16S rRNA gene and genomic sequence comparison revealed that the four strains belong to the genus
Gordonia
, most closely related to
G. neofelifaecis
NRRL B-59395T(98.2–98.3% sequence similarity) on the EzBioCloud database. The G+C contents of strains HY002T and HY366T based on genomic DNA were 66.5 and 66.9%, respectively. The DNA–DNA relatedness values between the two types strains and members of the genus
Gordonia
were far below 70 % (18.6–23.1 %). All genotypic and phenotypic data indicated that the four strains are representatives of two novel separate species, for which the names Gordonia zhenghanii sp. nov. and Gordonia liuliyuniae sp. nov. are proposed, with HY002T (=CGMCC 4 7757T=JCM 34 878T) and HY366T (=CGMCC 1 19146T=JCM 34 879T) as the respective type strains.
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Affiliation(s)
- Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jian Gong
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Lingzhi Dong
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jing Yang
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shan Lu
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xin-He Lai
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu 476000, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Dong Jin
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jianguo Xu
- Peking University School of Public Health, Beijing 100083, PR China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Research Institute of Public Health, Nankai University, Tianjin 300350, PR China
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23
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Riesco R, Rose JJA, Batinovic S, Petrovski S, Sánchez-Juanes F, Seviour RJ, Goodfellow M, Trujillo ME. Gordonia pseudamarae sp. nov., a home for novel actinobacteria isolated from stable foams on activated sludge wastewater treatment plants. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The taxonomic status of two
Gordonia
strains, designated BEN371 and CON9T, isolated from stable foams on activated sludge plants was the subject of a polyphasic study which also included the type strains of
Gordonia
species and three authenticated
Gordonia amarae
strains recovered from such foams. Phylogenetic analyses of 16S rRNA gene sequences showed that these isolates formed a compact cluster suggesting a well-supported lineage together with a second branch containing the
G. amarae
strains. A phylogenomic tree based on sequences of 92 core genes extracted from whole genome sequences of the isolates, the
G. amarae
strains and
Gordonia
type strains confirmed the assignment of the isolates and the
G. amarae
strains to separate but closely associated lineages. Average nucleotide index (ANI) and digital DNA–DNA hybridisation (dDDH) similarities showed that BEN371 and CON9T belonged to the same species and had chemotaxonomic and morphological features consistent with their assignment to the genus
Gordonia
. The isolates and the
G. amarae
strains were distinguished using a range of phenotypic features and by low ANI and dDDH values of 84.2 and 27.0 %, respectively. These data supplemented with associated genome characteristics show that BEN371 and CON9T represent a novel species of the genus
Gordonia
. The name proposed for members of this taxon is Gordonia pseudamarae sp. nov. with isolate CON9T (=DSM 43602T=JCM 35249T) as the type strain.
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Affiliation(s)
- Raúl Riesco
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
| | - Jayson J. A. Rose
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Steven Batinovic
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Steve Petrovski
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Fernando Sánchez-Juanes
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, CSIC, Salamanca, Spain
- Department of Biochemistry and Molecular Biology, University of Salamanca, Salamanca, Spain
| | - Robert J. Seviour
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
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24
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Jaishankar J, Keshav A, Jayaram B, Chavan S, Srivastava P. Characterization of divergent promoters PmaiA and Phyd from Gordonia: Co-expression and regulation by CRP. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194843. [PMID: 35840055 DOI: 10.1016/j.bbagrm.2022.194843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Divergent promoters are often responsible for controlling gene expression of related genes of the same pathway or for coordinating regulation at different time points. There are relatively few reports on characterization of divergent promoters in bacteria. In the present study, microarray profiling was carried out to analyze gene expression during growth of Gordonia sp. IITR100, which led to the identification of 35 % of adjacent gene candidates that are divergently transcribed. We focus here on the in-depth characterization of one such pair of genes. Two divergent promoters, PmaiA and Phyd, drive the expression of genes encoding maleate cis-trans isomerase (maiA) and hydantoinase (hyd), respectively. Our findings reveal asymmetric promoter activity with higher activity in the reverse orientation (Phyd) as compared to the forward orientation (PmaiA). Minimal promoter region for each orientation was identified by deletion mapping. Deletion of a 5'-untranslated region of each gene resulted in an increase in promoter activity. A putative binding site for CRP (Catabolite Repressor Protein) transcription regulator was also identified in the 80 bp common regulatory region between the -35 hexamers of the two promoters. The results of this study suggest that CRP-mediated repression of PmaiA occurs only in the cells grown in glucose. Phyd, on the other hand, is not repressed by CRP. However, deletion of the CRP binding site located between -95 to -110 upstream to the transcription start site of the maiA gene resulted in increased activity of PmaiA and decreased activity of Phyd. A single CRP binding site, therefore, affects the two promoters differently.
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Affiliation(s)
- Jananee Jaishankar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Aditi Keshav
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Bijjiga Jayaram
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Sourabh Chavan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Preeti Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India.
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25
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Versoza CJ, Howell AA, Aftab T, Blanco M, Brar A, Chaffee E, Howell N, Leach W, Lobatos J, Luca M, Maddineni M, Mirji R, Mitra C, Strasser M, Munig S, Patel Z, So M, Sy M, Weiss S, Pfeifer SP. Comparative Genomics of Closely-Related Gordonia Cluster DR Bacteriophages. Viruses 2022; 14:v14081647. [PMID: 36016269 PMCID: PMC9413003 DOI: 10.3390/v14081647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/16/2022] [Accepted: 07/25/2022] [Indexed: 12/10/2022] Open
Abstract
Bacteriophages infecting bacteria of the genus Gordonia have increasingly gained interest in the scientific community for their diverse applications in agriculture, biotechnology, and medicine, ranging from biocontrol agents in wastewater management to the treatment of opportunistic pathogens in pulmonary disease patients. However, due to the time and costs associated with experimental isolation and cultivation, host ranges for many bacteriophages remain poorly characterized, hindering a more efficient usage of bacteriophages in these areas. Here, we perform a series of computational genomic inferences to predict the putative host ranges of all Gordonia cluster DR bacteriophages known to date. Our analyses suggest that BiggityBass (as well as several of its close relatives) is likely able to infect host bacteria from a wide range of genera—from Gordonia to Nocardia to Rhodococcus, making it a suitable candidate for future phage therapy and wastewater treatment strategies.
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Affiliation(s)
- Cyril J. Versoza
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Abigail A. Howell
- Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Tanya Aftab
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Madison Blanco
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Akarshi Brar
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Elaine Chaffee
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Nicholas Howell
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Willow Leach
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Jackelyn Lobatos
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Michael Luca
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Meghna Maddineni
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Ruchira Mirji
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Corinne Mitra
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Maria Strasser
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Saige Munig
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Zeel Patel
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Minerva So
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Makena Sy
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Sarah Weiss
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Susanne P. Pfeifer
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA;
- Correspondence:
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26
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Baek G, Rossi R, Saikaly PE, Logan BE. High-rate microbial electrosynthesis using a zero-gap flow cell and vapor-fed anode design. WATER RESEARCH 2022; 219:118597. [PMID: 35609490 DOI: 10.1016/j.watres.2022.118597] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/08/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Microbial electrosynthesis (MES) cells use renewable energy to convert carbon dioxide into valuable chemical products such as methane and acetate, but chemical production rates are low and pH changes can adversely impact biocathodes. To overcome these limitations, an MES reactor was designed with a zero-gap electrode configuration with a cation exchange membrane (CEM) to achieve a low internal resistance, and a vapor-fed electrode to minimize pH changes. Liquid catholyte was pumped through a carbon felt cathode inoculated with anaerobic digester sludge, with humidified N2 gas flowing over the abiotic anode (Ti or C with a Pt catalyst) to drive water splitting. The ohmic resistance was 2.4 ± 0.5 mΩ m2, substantially lower than previous bioelectrochemical systems (20-25 mΩ m2), and the catholyte pH remained near-neutral (6.6-7.2). The MES produced a high methane production rate of 2.9 ± 1.2 L/L-d (748 mmol/m2-d, 17.4 A/m2; Ti/Pt anode) at a relatively low applied voltage of 3.1 V. In addition, acetate was produced at a rate of 940 ± 250 mmol/m2-d with 180 ± 30 mmol/m2-d for propionate. The biocathode microbial community was dominated by the methanogens of the genus Methanobrevibacter, and the acetogen of the genus Clostridium sensu stricto 1. These results demonstrate the utility of this zero-gap cell and vapor-fed anode design for increasing rates of methane and chemical production in MES.
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Affiliation(s)
- Gahyun Baek
- Department of Civil and Environmental Engineering, Penn State University, 231Q Sackett Building, University Park, PA 16802, United States; Environmental Research Group, Research Institute of Industrial Science and Technology (RIST), 67 Cheongam-ro, Nam-gu, Pohang-si, Gyeongsangbuk-do, 37673 Republic of Korea
| | - Ruggero Rossi
- Department of Civil and Environmental Engineering, Penn State University, 231Q Sackett Building, University Park, PA 16802, United States
| | - Pascal E Saikaly
- Environmental Science and Engineering Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Saudi Arabia
| | - Bruce E Logan
- Department of Civil and Environmental Engineering, Penn State University, 231Q Sackett Building, University Park, PA 16802, United States.
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27
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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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28
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Kobayashi T, Otake S, Mori T, Hasegawa D, Kosaka Y, Ohkusu K, Kasai M. A pediatric case of Gordonia otitidis bacteremia detected by long-term blood culture. J Infect Chemother 2022; 28:1427-1429. [PMID: 35724915 DOI: 10.1016/j.jiac.2022.06.008] [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: 03/27/2022] [Revised: 06/11/2022] [Accepted: 06/14/2022] [Indexed: 11/24/2022]
Abstract
For immunocompromised patients receiving chemotherapy or bone mallow transplantation, slow-growing bacteria should also be considered one of the pathogenic microorganisms. However, there is no evidence pertaining to the microbiological tests associated with a patient with febrile neutropenia before peripheral blood stem cell harvest (PBSCH). We report a case of a 4-year-old cancer-bearing female presenting with a catheter-related bloodstream infection due to Gordonia otitidis. We detected G. otitidis from long-term blood cultures for approximately 6 days and prevented iatrogenic bacteremia by identifying the same organism from the culture of the PBSC sample and postponing the scheduled PBSCH. If febrile neutropenia occurs before PBSCH, we should collect multiple sets of blood cultures and culture them for a longer period.
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Affiliation(s)
- Takao Kobayashi
- Division of Infectious Diseases, Department of Pediatrics, Kobe Children's Hospital, Hyogo, Japan
| | - Shogo Otake
- Division of Infectious Diseases, Department of Pediatrics, Kobe Children's Hospital, Hyogo, Japan.
| | - Takeshi Mori
- Department of Hematology and Oncology, Children's Cancer Center, Kobe Children's Hospital, Hyogo, Japan
| | - Daiichiro Hasegawa
- Department of Hematology and Oncology, Children's Cancer Center, Kobe Children's Hospital, Hyogo, Japan
| | - Yoshiyuki Kosaka
- Department of Hematology and Oncology, Children's Cancer Center, Kobe Children's Hospital, Hyogo, Japan
| | - Kiyofumi Ohkusu
- Department of Microbiology, Tokyo Medical University, Hyogo, Japan
| | - Masashi Kasai
- Division of Infectious Diseases, Department of Pediatrics, Kobe Children's Hospital, Hyogo, Japan
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29
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Yang Z, Zhang Z, Chen M, Liu Z. Gordonia crocea sp. nov. Isolated from Wound Infection After Pacemaker Implantation: Case Report and Literature Review. Infect Drug Resist 2022; 15:2915-2920. [PMID: 35698534 PMCID: PMC9188390 DOI: 10.2147/idr.s368903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/31/2022] [Indexed: 12/02/2022] Open
Abstract
Gordonia is a recognized pathogen in patients with immunodeficiency and a normal immune response, which can cause bacteremia, endocarditis, peritonitis and pulmonary infection. We report a case of wound infection after pacemaker implantation caused by Gordonia crocea. Matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF MS) was routinely used to identify the pathogen, and the results showed that the pathogen could not be accurately identified in the MALDI-TOF database at present. The 16S rRNA gene of the pathogen was further sequenced, and the result was Gordonia crocea. To the best of our knowledge, this is the first reported case of human infection caused by Gordonia crocea.
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Affiliation(s)
- Zhulan Yang
- Department of Clinical Laboratory, Southwest Hospital, Army Medical University, Chongqing, People’s Republic of China
| | - Zhen Zhang
- Department of Clinical Laboratory, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, People’s Republic of China
| | - Ming Chen
- Department of Clinical Laboratory, Southwest Hospital, Army Medical University, Chongqing, People’s Republic of China
| | - Zhiyong Liu
- Department of Clinical Laboratory, Southwest Hospital, Army Medical University, Chongqing, People’s Republic of China
- Correspondence: Zhiyong Liu; Ming Chen, Email ;
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Donati VL, Madsen L, Middelboe M, Strube ML, Dalsgaard I. The Gut Microbiota of Healthy and Flavobacterium psychrophilum-Infected Rainbow Trout Fry Is Shaped by Antibiotics and Phage Therapies. Front Microbiol 2022; 13:771296. [PMID: 35620089 PMCID: PMC9128845 DOI: 10.3389/fmicb.2022.771296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 03/07/2022] [Indexed: 01/15/2023] Open
Abstract
In the aquaculture sector, there is an increased interest in developing environmentally friendly alternatives to antibiotics in the treatment and prevention of bacterial infections. This requires an understanding of the effects of different treatments on the fish microbiota as a measure for improving the fish health status. In this study, we focused on the freshwater pathogen Flavobacterium psychrophilum and investigated the effects of antibiotics (florfenicol) and phage therapies on the gut microbiota of healthy and infected rainbow trout fry (1–2 g). Florfenicol-coated feed was administered for 10 days, starting two days after the infection procedure. A two-component mix of phage targeting F. psychrophilum (FpV4 and FPSV-D22) was continuously delivered by feed with a prophylactic period of 12 days. Samples of the distal intestine were collected over time (day -1 and 1, 8, and 33 days post-infection) and analyzed by community analysis targeting the 16S rRNA gene (V3–V4 region). Results showed the dysbiosis effect caused both by the infection and by florfenicol administration. Shifts in the overall composition were detected by β-diversity analysis, and changes in specific populations were observed during taxonomic mapping. Measures of α-diversity were only affected in infected fish (large variation observed 1 and 8 dpi). These community alterations disappeared again when fish recovered from the infection and the antibiotic treatment was terminated (33 dpi). Interestingly, phage addition altered the microbiota of the fish independently of the presence of their target bacterium. The overall gut bacterial community in fish fed phage-treated feed was different from the controls at each time point as revealed by β-diversity analysis. However, it was not possible to identify specific bacterial populations responsible for these changes except for an increase of lactic acid bacteria 33 dpi. Overall, the results indicate that the administered phages might affect the complex network of phage-bacteria interactions in the fish gut. Nevertheless, we did not observe negative effects on fish health or growth, and further studies should be directed in understanding if these changes are beneficial or not for the fish health with an additional focus on the host immune response.
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Affiliation(s)
- Valentina Laura Donati
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lone Madsen
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mathias Middelboe
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Inger Dalsgaard
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
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Yang Z, Li H, Li N, Sardar MF, Song T, Zhu H, Xing X, Zhu C. Dynamics of a Bacterial Community in the Anode and Cathode of Microbial Fuel Cells under Sulfadiazine Pressure. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19106253. [PMID: 35627790 PMCID: PMC9141142 DOI: 10.3390/ijerph19106253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 12/10/2022]
Abstract
Microbial fuel cells (MFCs) could achieve the removal of antibiotics and generate power in the meantime, a process in which the bacterial community structure played a key role. Previous work has mainly focused on microbes in the anode, while their role in the cathode was seldomly mentioned. Thus, this study explored the bacterial community of both electrodes in MFCs under sulfadiazine (SDZ) pressure. The results showed that the addition of SDZ had a limited effect on the electrochemical performance, and the maximum output voltage was kept at 0.55 V. As the most abundant phylum, Proteobacteria played an important role in both the anode and cathode. Among them, Geobacter (40.30%) worked for power generation, while Xanthobacter (11.11%), Bradyrhizobium (9.04%), and Achromobacter (7.30%) functioned in SDZ removal. Actinobacteria mainly clustered in the cathode, in which Microbacterium (9.85%) was responsible for SDZ removal. Bacteroidetes, associated with the degradation of SDZ, showed no significant difference between the anode and cathode. Cathodic and part of anodic bacteria could remove SDZ efficiently in MFCs through synergistic interactions and produce metabolites for exoelectrogenic bacteria. The potential hosts of antibiotic resistance genes (ARGs) presented mainly at the anode, while cathodic bacteria might be responsible for ARGs reduction. This work elucidated the role of microorganisms and their synergistic interaction in MFCs and provided a reference to generate power and remove antibiotics using MFCs.
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Affiliation(s)
- Zhenzhen Yang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Z.Y.); (M.F.S.); (T.S.); (C.Z.)
| | - Hongna Li
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Z.Y.); (M.F.S.); (T.S.); (C.Z.)
- Correspondence: ; Tel.: +86-10-8210-9561
| | - Na Li
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China;
| | - Muhammad Fahad Sardar
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Z.Y.); (M.F.S.); (T.S.); (C.Z.)
| | - Tingting Song
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Z.Y.); (M.F.S.); (T.S.); (C.Z.)
| | - Hong Zhu
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing 100096, China;
| | - Xuan Xing
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China;
| | - Changxiong Zhu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Z.Y.); (M.F.S.); (T.S.); (C.Z.)
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A New Biosurfactant/Bioemulsifier from Gordonia alkanivorans Strain 1B: Production and Characterization. Processes (Basel) 2022. [DOI: 10.3390/pr10050845] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Biosurfactants and bioemulsifiers (BS/BE) are naturally synthesized molecules, which can be used as alternatives to traditional detergents. These molecules are commonly produced by microorganisms isolated from hydrocarbon-rich environments. Gordonia alkanivorans strain 1B was originally found in such an environment, however little was known about its abilities as a BS/BE producer. The goal of this work was to access the potential of strain 1B as a BS/BE producer and perform the initial characterization of the produced compounds. It was demonstrated that strain 1B was able to synthesize lipoglycoprotein compounds with BS/BE properties, both extracellularly and adhered to the cells, without the need for a hydrophobic inducer, producing emulsion in several different hydrophobic phases. Using a crude BS/BE powder, the critical micelle concentration was determined (CMC = 16.94 mg/L), and its capacity to reduce the surface tension to a minimum of 35.63 mN/m was demonstrated, surpassing many commercial surfactants. Moreover, after dialysis, emulsification assays revealed an activity similar to that of Triton X-100 in almond and sunflower oils. In benzene, the E24 value attained was 83.45%, which is 30% greater than that of the commercial alternative. The results obtained highlight for the presence of promising novel BS/BE produced by strain 1B.
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Zargar AN, Mishra S, Kumar M, Srivastava P. Isolation and chemical characterization of the biosurfactant produced by Gordonia sp. IITR100. PLoS One 2022; 17:e0264202. [PMID: 35421133 PMCID: PMC9009618 DOI: 10.1371/journal.pone.0264202] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 02/05/2022] [Indexed: 11/18/2022] Open
Abstract
Biosurfactants are amphipathic molecules produced from microorganisms. There are relatively few species known where the detailed chemical characterization of biosurfactant has been reported. Here, we report isolation and chemical characterization of the biosurfactant produced by a biodesulfurizing bacterium Gordonia sp. IITR100. Biosurfactant production was determined by performing oil spreading, drop-collapse, Emulsion index (E24), and Bacterial adhesion to hydrocarbons (BATH) assay. The biosurfactant was identified as a glycolipid by LCMS and GCMS analysis. The chemical structure was further confirmed by performing FTIR and NMR of the extracted biosurfactant. The emulsion formed by the biosurfactant was found to be stable between temperatures of 4°C to 30°C, pH of 6 to 10 and salt concentrations up to 2%. It was successful in reducing the surface tension of the aqueous media from 61.06 mN/m to 36.82 mN/m. The biosurfactant produced can be used in petroleum, detergents, soaps, the food and beverage industry and the healthcare industry.
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Affiliation(s)
- Arif Nissar Zargar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Sarthak Mishra
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Manoj Kumar
- Indian Oil Corporation, R&D Centre, Faridabad, India
| | - Preeti Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
- * E-mail: ,
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Gordonia species as a rare pathogen isolated from milk of dairy cows with mastitis. Sci Rep 2022; 12:6028. [PMID: 35411009 PMCID: PMC9001696 DOI: 10.1038/s41598-022-09340-4] [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: 06/06/2021] [Accepted: 03/21/2022] [Indexed: 11/24/2022] Open
Abstract
While Gordonia species have long been known to cause severe inflammation in humans, the pathogenic effects of Gordonia species in veterinary medicine have rarely been described. Between 2010 and 2019, we collected microorganisms of the genus Gordonia isolated from milk samples from dairy cows with mastitis. We describe the growth properties of these microorganisms and their prevalence, virulence factors and susceptibility to antimicrobial agents. From 31,534 quarter milk samples processed by standard culture methods, 27 isolates of Gordonia species (0.086% prevalence) were identified by a molecular phenotyping method. The isolates originated from 17 farms in 12 districts of the Czech Republic. Twenty-one isolates were tested for susceptibility to 7 antimicrobials by the disc diffusion method. Notably, 100% of these isolates were susceptible to streptomycin and neomycin, 85.7% to cefovecin and tetracycline, 76.2% to penicillin G, 47.6% to trimethoprim/sulfamethoxazole and 0% to clindamycin. The species was determined to be Gordonia paraffinivorans by whole genome sequencing for 9 isolates (from 8 farms in 7 districts). These isolates showed the highest similarity to two reference strains from the environment. In all these isolates, we identified genes encoding virulence factors that are very similar to genes encoding virulence factors expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis. However, genome analysis revealed 61 unique genes in all 9 sequenced isolates.
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From Rest to Growth: Life Collisions of Gordonia polyisoprenivorans 135. Microorganisms 2022; 10:microorganisms10020465. [PMID: 35208919 PMCID: PMC8879720 DOI: 10.3390/microorganisms10020465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
In the process of evolution, living organisms develop mechanisms for population preservation to survive in unfavorable conditions. Spores and cysts are the most obvious examples of dormant forms in microorganisms. Non-spore-forming bacteria are also capable of surviving in unfavorable conditions, but the patterns of their behavior and adaptive reactions have been studied in less detail compared to spore-forming organisms. The purpose of this work was to study the features of transition from dormancy to active vegetative growth in one of the non-spore-forming bacteria, Gordonia polisoprenivorans 135, which is known as a destructor of such aromatic compounds as benzoate, 3-chlorobenzoate, and phenol. It was shown that G. polyisoprenivorans 135 under unfavorable conditions forms cyst-like cells with increased thermal resistance. Storage for two years does not lead to complete cell death. When the cells were transferred to fresh nutrient medium, visible growth was observed after 3 h. Immobilized cells stored at 4 °C for at least 10 months regenerated their metabolic activity after only 30 min of aeration. A study of the ultrathin organization of resting cells by transmission electron microscopy combined with X-ray microanalysis revealed intracytoplasmic electron-dense spherical membrane ultrastructures with significant similarity to previously described acidocalcisomas. The ability of some resting G. polyisoprenivorans 135 cells in the population to secrete acidocalcisome-like ultrastructures into the extracellular space was also detected. These structures contain predominantly calcium (Ca) and, to a lesser extent, phosphorus (P), and are likely to serve as depots of vital macronutrients to maintain cell viability during resting and provide a quick transition to a metabolically active state under favorable conditions. The study revealed the features of transitions from active growth to dormant state and vice versa of non-spore-forming bacteria G. polyisoprenivorans 135 and the possibility to use them as the basis of biopreparations with a long shelf life.
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Mechanistic Understanding of Gordonia sp. in Biodesulfurization of Organosulfur Compounds. Curr Microbiol 2022; 79:82. [PMID: 35107610 DOI: 10.1007/s00284-022-02770-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 01/18/2022] [Indexed: 11/03/2022]
Abstract
Although conventional oil refining process like hydrodesulfurization (HDS) is capable of removing sulfur compounds present in crude oil, it cannot desulfurize recalcitrant organosulfur compounds such as dibenzothiophenes (DBTs), benzothiophenes (BTs), etc. Biodesulfurization (BDS) is a process of selective removal of sulfur moieties from DBT or BT by desulfurizing microbes. Therefore, BDS can be used as a complementary and economically feasible technology to achieve deep desulfurization of crude oil without affecting the calorific value. In the recent past, members of biodesulfurizing actinomycete genus Gordonia, isolated from versatile environments like soil, activated sludge, human beings etc. have been greatly exploited in the field of petroleum refining technology. The bacterium Gordonia sp. is slightly acid-fast and has been used for unconventional but potential oil refining processes like BDS in petroleum refineries. Gordonia sp. is unique in a way, that it can desulfurize both aliphatic and aromatic organosulfurs without affecting the calorific value of hydrocarbon molecules. Till date, approximately six different species and nineteen strains of the genus Gordonia have been recognized for BDS activity. Various factors such as enzyme specificity, availability of essential cofactors, feedback inhibition, toxicity of organic pollutants and the oil-water separations limit the desulfurization rate of microbial biocatalyst and influence its commercial applications. The current review selectively highlights the role of this versatile genus in removing sulfur from fossil fuels, mechanisms and future prospects on sustainable environment friendly technologies for crude oil refining.
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Genome Sequences of Gordonia rubripertincta Bacteriophages AnarQue and Figliar. Microbiol Resour Announc 2022; 11:e0108521. [PMID: 35049345 PMCID: PMC8772589 DOI: 10.1128/mra.01085-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AnarQue and Figliar are bacteriophages identified from the host bacterium Gordonia rubripertincta NRRL B-16540. AnarQue is circularly permuted and has a length of 61,822 bp; it is assigned to cluster DR. Figliar has a 3' sticky overhang and a length of 61,147 bp; it is assigned to cluster DJ.
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Nwaedozie S, Mojarrab JN, Gopinath P, Fritsche T, Nasser RM. Sternal osteomyelitis caused by Gordonia bronchialis in an immunocompetent patient following coronary artery bypass surgery. IDCases 2022; 29:e01548. [PMID: 35801008 PMCID: PMC9253898 DOI: 10.1016/j.idcr.2022.e01548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 11/15/2022] Open
Affiliation(s)
- Somto Nwaedozie
- Department of Internal Medicine, Marshfield Clinic Health System – Marshfield, Marshfield, WI 54449, USA
- Correspondence to: Department of Internal Medicine, Marshfield Clinic Health System – Marshfield, 1,000 North Oak Avenue 3K2, Marshfield, WI 54449, USA.
| | - Javad Najjar Mojarrab
- Department of Internal Medicine, Marshfield Clinic Health System – Marshfield, Marshfield, WI 54449, USA
| | - Prathima Gopinath
- Department of Internal Medicine, Marshfield Clinic Health System – Marshfield, Marshfield, WI 54449, USA
| | - Thomas Fritsche
- Department of Pathology, Marshfield Clinic Health System – Marshfield, Marshfield, WI 54449, USA
| | - Rana M. Nasser
- Department of Infectious Disease, Marshfield Clinic Health System – Marshfield, Marshfield, WI 54449, USA
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Bruno V, Tjon J, Lin S, Groves H, Kazmi K, Zappitelli M, Harvey E. Peritoneal dialysis-related peritonitis caused by Gordonia bronchialis: first pediatric report. Pediatr Nephrol 2022; 37:217-220. [PMID: 34633526 PMCID: PMC8503381 DOI: 10.1007/s00467-021-05313-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 09/21/2021] [Accepted: 09/21/2021] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Gordonia species, aerobic, weakly acid-fast, Gram-positive bacilli, are a rare cause of peritonitis in patients undergoing peritoneal dialysis (PD). We report the first pediatric case of PD-related peritonitis caused by Gordonia bronchialis. CASE PRESENTATION A 13-year-old girl with chronic kidney disease (CKD) stage 5D, on continuous cycling PD (CCPD) for 8 years, presented with cloudy PD effluent, with no abdominal discomfort or fever. Intra-peritoneal (IP) loading doses of vancomycin and ceftazidime were started at home after obtaining a PD effluent sample, which showed WBC 2,340 × 10 /L (59% neutrophils) and Gram-positive bacilli. On admission, she was clinically well and afebrile, with no history of methicillin-resistant Staphylococcus aureus (MRSA) infection, so vancomycin was discontinued, and IP ceftazidime and cefazolin were started, following a loading dose of intravenous cefazolin. Gordonia species grew after 5 days of incubation and later identified as Gordonia bronchialis. IP vancomycin was restarted as monotherapy, empirically for a total of 3 weeks therapy. A 2-week course of oral ciprofloxacin was added, based on susceptibility testing. PD catheter replacement was advised due to the risk of recurrence but was refused. A relapse occurred 16 days after discontinuing antibiotics, successfully treated with a 2-week course of IP ceftazidime and vancomycin. The PD catheter was removed and hemodialysis initiated. She received a further 2-week course of oral ciprofloxacin and amoxicillin-clavulanate post PD catheter removal. CONCLUSIONS Gordonia bronchialis is an emerging pathogen in PD peritonitis and appears to be associated with a high risk of relapse. PD catheter replacement is strongly suggested.
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Affiliation(s)
- Valentina Bruno
- Division of Nephrology, The Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada. .,Department of Paediatrics, University of Toronto, Toronto, ON, Canada.
| | - James Tjon
- Department of Pharmacy, The Hospital for Sick Children, Toronto, ON Canada
| | - Sandy Lin
- Department of Nursing, The Hospital for Sick Children, Toronto, ON Canada
| | - Helen Groves
- Department of Paediatrics, University of Toronto, Toronto, ON Canada ,Division of Infectious Diseases, The Hospital for Sick Children, Toronto, ON Canada
| | - Kescha Kazmi
- Department of Paediatrics, University of Toronto, Toronto, ON Canada ,Division of Infectious Diseases, The Hospital for Sick Children, Toronto, ON Canada
| | - Michael Zappitelli
- Division of Nephrology, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8 Canada ,Department of Paediatrics, University of Toronto, Toronto, ON Canada
| | - Elizabeth Harvey
- Division of Nephrology, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8 Canada ,Department of Paediatrics, University of Toronto, Toronto, ON Canada
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Liu N, Maser E, Zhang T. Genomic analysis of Gordonia polyisoprenivorans strain R9, a highly effective 17 beta-estradiol- and steroid-degrading bacterium. Chem Biol Interact 2021; 350:109685. [PMID: 34653397 DOI: 10.1016/j.cbi.2021.109685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 09/25/2021] [Accepted: 10/02/2021] [Indexed: 10/20/2022]
Abstract
The increasing levels of estrogens and pollution by other steroids pose considerable challenges to the environment. In this study, the genome of Gordonia polyisoprenivorans strain R9, one of the most effective 17 beta-estradiol- and steroid-degrading bacteria, was sequenced and annotated. The circular chromosome of G. polyisoprenivorans R9 was 6,033,879 bp in size, with an average GC content of 66.91%. More so, 5213 putative protein-coding sequences, 9 rRNA, 49 tRNA, and 3 sRNA genes were predicted. The core-pan gene evolutionary tree for the genus Gordonia showed that G. polyisoprenivorans R9 is clustered with G. polyisoprenivorans VH2 and G. polyisoprenivorans C, with 93.75% and 93.8% similarity to these two strains, respectively. Altogether, the three G. polyisoprenivorans strains contained 3890 core gene clusters. Strain R9 contained 785 specific gene clusters, while 501 and 474 specific gene clusters were identified in strains VH2 and C, respectively. Furthermore, whole genome analysis revealed the existence of the steroids and estrogens degradation pathway in the core genome of all three G. polyisoprenivorans strains, although the G. polyisoprenivorans R9 genome contained more specific estrogen and steroid degradation genes. In strain R9, 207 ABC transporters, 95 short-chain dehydrogenases (SDRs), 26 monooxygenases, 21 dioxygenases, 7 aromatic ring-hydroxylating dioxygenases, and 3 CoA esters were identified, and these are very important for estrogen and steroid transport, and degradation. The results of this study could enhance our understanding of the role of G. polyisoprenivorans R9 in estradiol and steroid degradation as well as evolution within the G. polyisoprenivorans species.
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Affiliation(s)
- Na Liu
- Key Laboratory of Groundwater Resources and Environment (Jilin University), Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130021, China
| | - Edmund Maser
- Institute of Toxicology and Pharmacology for Natural Scientists, University Medical School, Schleswig-Holstein, Campus Kiel, Brunswiker Str. 10, D-24105 Kiel, Germany
| | - Tingdi Zhang
- Key Laboratory of Groundwater Resources and Environment (Jilin University), Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130021, China.
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Sarkar B, Mandal S. Gordonia sp. BSTG01 isolated from Hevea brasiliensis plantation efficiently degrades polyisoprene (rubber). 3 Biotech 2021; 11:508. [PMID: 34881168 DOI: 10.1007/s13205-021-03063-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/09/2021] [Indexed: 12/17/2022] Open
Abstract
Polyisoprene is the principal constituent of rubber latex which has been estimated globally as one of the major solid wastes. Bacterial bioremediation of this solid waste remains a major point of interest for scientists. This study reports a Gram-positive, non-motile, non-spore-forming actinomycete Gordonia sp. BSTG01, isolated from the bark of Hevea brasiliensis of a rubber plantation garden can considerably degrade natural rubber (NR) and synthetic polyisoprene rubber (SR). Scanning electron microscopy showed adhesive colonization of strain BSTG01 on both natural and synthetic rubber surface, conflating into the rubber and forming a biofilm. Rubber-dependent growth of the strain was examined by the decrease of rubber mass and increase of its total protein content in a time-dependent manner. Degradation was also verified by Schiff's reagent which confirms the appearance of aldehydes in the culture media. Fourier transform infrared spectroscopy including the attenuated total reflectance with the NR and SR pieces overgrown by the isolate revealed variations of the overall chemicals arising on the polyisoprene backbone due to the degradation of rubber by the strain BSTG01. Isolate BSTG01 (MTCC 13159) is a strain of Gordonia and this is the first strain isolated from unexplored rubber plantation area with considerable rubber degradation properties. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03063-5.
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Affiliation(s)
- Biraj Sarkar
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019 India
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019 India
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Cassarini M, Besaury L, Rémond C. Valorisation of wheat bran to produce natural pigments using selected microorganisms. J Biotechnol 2021; 339:81-92. [PMID: 34364925 DOI: 10.1016/j.jbiotec.2021.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 11/27/2022]
Abstract
Pigments are compounds with highly diverse structures and wide uses, which production is increasing worldwide. An eco-friendly method of bioproduction is to use the ability of some microorganisms to ferment on renewable carbon sources. Wheat bran (WB) is a cheap and abundant lignocellulosic co-product of low recalcitrance to biological conversion. Microbial candidates with theoretical ability to degrade WB were first preselected using specific databases. The microorganisms were Ashbya gossypii (producing riboflavin), Chitinophaga pinensis (producing flexirubin), Chromobacterium vaccinii (violacein) and Gordonia alkanivorans (carotenoids). Growth was shown for each on minimal salt medium supplemented with WB at 5 g.L-1. Activities of the main enzymes consuming WB were measured, showing leucine amino-peptidase (up to 8.45 IU. mL-1) and β-glucosidase activities (none to 6.44 IU. mL-1). This was coupled to a FTIR (Fourier Transform Infra-Red) study of the WB residues that showed main degradation of the WB protein fraction for C. pinensis, C. vaccinii and G. alkanivorans. Production of the pigments on WB was assessed for all the strains except Ashbya, with values of production reaching up to 1.47 mg.L-1. The polyphasic approach used in this study led to a proof of concept of pigment production from WB as a cheap carbon source.
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Affiliation(s)
- Mathieu Cassarini
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France.
| | - Ludovic Besaury
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France.
| | - Caroline Rémond
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France.
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Basik AA, Sanglier JJ, Yeo CT, Sudesh K. Microbial Degradation of Rubber: Actinobacteria. Polymers (Basel) 2021; 13:polym13121989. [PMID: 34204568 PMCID: PMC8235351 DOI: 10.3390/polym13121989] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 01/25/2023] Open
Abstract
Rubber is an essential part of our daily lives with thousands of rubber-based products being made and used. Natural rubber undergoes chemical processes and structural modifications, while synthetic rubber, mainly synthetized from petroleum by-products are difficult to degrade safely and sustainably. The most prominent group of biological rubber degraders are Actinobacteria. Rubber degrading Actinobacteria contain rubber degrading genes or rubber oxygenase known as latex clearing protein (lcp). Rubber is a polymer consisting of isoprene, each containing one double bond. The degradation of rubber first takes place when lcp enzyme cleaves the isoprene double bond, breaking them down into the sole carbon and energy source to be utilized by the bacteria. Actinobacteria grow in diverse environments, and lcp gene containing strains have been detected from various sources including soil, water, human, animal, and plant samples. This review entails the occurrence, physiology, biochemistry, and molecular characteristics of Actinobacteria with respect to its rubber degrading ability, and discusses possible technological applications based on the activity of Actinobacteria for treating rubber waste in a more environmentally responsible manner.
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Affiliation(s)
- Ann Anni Basik
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia;
- Sarawak Biodiversity Centre, Km. 20 Jalan Borneo Heights, Semengoh, Kuching, Sarawak 93250, Malaysia; (J.-J.S.); (C.T.Y.)
| | - Jean-Jacques Sanglier
- Sarawak Biodiversity Centre, Km. 20 Jalan Borneo Heights, Semengoh, Kuching, Sarawak 93250, Malaysia; (J.-J.S.); (C.T.Y.)
| | - Chia Tiong Yeo
- Sarawak Biodiversity Centre, Km. 20 Jalan Borneo Heights, Semengoh, Kuching, Sarawak 93250, Malaysia; (J.-J.S.); (C.T.Y.)
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia;
- Correspondence: ; Tel.: +60-4-6534367; Fax: +60-4-6565125
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Santoro D, Archer L, Fagman L. Intradermal immunotherapy with actinomycetales preparations as treatment for feline atopic syndrome: a randomized, placebo-controlled, double-blinded study. Vet Dermatol 2021; 32:638-e170. [PMID: 33890342 DOI: 10.1111/vde.12946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/13/2020] [Accepted: 12/05/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND Feline atopic syndrome (FAS) is a common disease. Single intradermal injections of heat-killed actinomycetales have shown beneficial effects in canine allergies. HYPOTHESIS/OBJECTIVE To evaluate the clinical effects of heat-killed actinomycetales [Gordonia bronchialis (GB) and Rodococcus coprophilus (RC)], alone or in combination, in FAS. METHODS AND MATERIALS Privately owned cats with a diagnosis of FAS were assigned randomly in three treatment groups (GB, RC and GB/RC combination) or placebo. Five intradermal injections were performed over a one year period. At each visit [Day (D)0, D20, D40, D60, D90, D180 and D365], clinical signs, global owner assessment score, use of rescue medications, clinical adverse effects, skin hydration and cutaneous pH were assessed. RESULTS Seventeen cats were enrolled. When compared to the placebo group and improvement in treatment GB was sustained from D90. When compared with D0 significant improvement in the GB group was seen from D60. Over one year, a complete remission of the clinical signs was seen in 30-67% of cats in the treatment groups. A reduction in the pruritus score was seen for RC after 365 days of treatment (P = 0.04). Differences in the other variables were not seen. CONCLUSIONS AND CLINICAL IMPORTANCE The use of multiple intradermal injections of heat-killed GB shows promise as effective and well-tolerated treatment for FAS. Because of the low cost and the lack of adverse effects, GB could be a beneficial treatment option for FAS. A larger study is needed to confirm these data and to evaluate the immunological changes occurring in the treated cats.
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Affiliation(s)
- Domenico Santoro
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, 2015 SW 16th Avenue, Gainesville, FL, 32610, USA
| | - Linda Archer
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, 2015 SW 16th Avenue, Gainesville, FL, 32610, USA
| | - Lana Fagman
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, 2015 SW 16th Avenue, Gainesville, FL, 32610, USA
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Complete and Circularized Bacterial Genome Sequence of Gordonia sp. Strain X0973. Microbiol Resour Announc 2021; 10:10/9/e01479-20. [PMID: 33664146 PMCID: PMC7936644 DOI: 10.1128/mra.01479-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gordonia sp. strain X0973 is a Gram-positive, weakly acid-fast, aerobic actinomycete obtained from a human abscess with Gordonia araii NBRC 100433T as its closest phylogenetic neighbor. Here, we report using Illumina MiSeq and PacBio reads to assemble the complete and circular genome sequence of 3.75 Mbp with 3,601 predicted coding sequences.
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Guerrero LD, Pérez MV, Orellana E, Piuri M, Quiroga C, Erijman L. Long-run bacteria-phage coexistence dynamics under natural habitat conditions in an environmental biotechnology system. THE ISME JOURNAL 2021; 15:636-648. [PMID: 33067586 PMCID: PMC8027832 DOI: 10.1038/s41396-020-00802-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 09/21/2020] [Accepted: 10/01/2020] [Indexed: 01/30/2023]
Abstract
Bacterial viruses are widespread and abundant across natural and engineered habitats. They influence ecosystem functioning through interactions with their hosts. Laboratory studies of phage-host pairs have advanced our understanding of phenotypic and genetic diversification in bacteria and phages. However, the dynamics of phage-host interactions have been seldom recorded in complex natural environments. We conducted an observational metagenomic study of the dynamics of interaction between Gordonia and their phages using a three-year data series of samples collected from a full-scale wastewater treatment plant. The aim was to obtain a comprehensive picture of the coevolution dynamics in naturally evolving populations at relatively high time resolution. Coevolution was followed by monitoring changes over time in the CRISPR loci of Gordonia metagenome-assembled genome, and reciprocal changes in the viral genome. Genome-wide analysis indicated low strain variability of Gordonia, and almost clonal conservation of the trailer end of the CRISPR loci. Incorporation of newer spacers gave rise to multiple coexisting bacterial populations. The host population carrying a shorter CRISPR locus that contain only ancestral spacers, which has not acquired newer spacers against the coexisting phages, accounted for more than half of the total host abundance in the majority of samples. Phages genome co-evolved by introducing directional changes, with no preference for mutations within the protospacer and PAM regions. Metagenomic reconstruction of time-resolved variants of host and viral genomes revealed how the complexity at the population level has important consequences for bacteria-phage coexistence.
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Affiliation(s)
- Leandro D. Guerrero
- grid.423606.50000 0001 1945 2152Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr Héctor N. Torres” (INGEBI-CONICET), Vuelta de Obligado 2490, C1428ADN Buenos Aires, Argentina
| | - María V. Pérez
- grid.423606.50000 0001 1945 2152Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr Héctor N. Torres” (INGEBI-CONICET), Vuelta de Obligado 2490, C1428ADN Buenos Aires, Argentina ,Agua y Saneamientos Argentinos S.A., Tucumán 752, C1049APP Buenos Aires, Argentina
| | - Esteban Orellana
- grid.423606.50000 0001 1945 2152Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr Héctor N. Torres” (INGEBI-CONICET), Vuelta de Obligado 2490, C1428ADN Buenos Aires, Argentina
| | - Mariana Piuri
- Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, CONICET, Intendente Güiraldes 2160, C1428EGA Buenos Aires, Argentina
| | - Cecilia Quiroga
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Facultad de Medicina, Universidad de Buenos Aires, CONICET, Paraguay 2155, C1121ABG Buenos Aires, Argentina
| | - Leonardo Erijman
- grid.423606.50000 0001 1945 2152Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr Héctor N. Torres” (INGEBI-CONICET), Vuelta de Obligado 2490, C1428ADN Buenos Aires, Argentina ,grid.7345.50000 0001 0056 1981Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires, Intendente Güiraldes 2160s, C1428EGA Buenos Aires, Argentina
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Complete Genome Sequence of Gordonia rubripertincta SD5, a Soil Bacterium Isolated from a Di-(2-Ethylhexyl) Phthalate-Degrading Enrichment Culture. Microbiol Resour Announc 2020; 9:9/45/e01087-20. [PMID: 33154014 PMCID: PMC7645669 DOI: 10.1128/mra.01087-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the complete genome sequence of Gordonia rubripertincta SD5, isolated from a soil-derived di-(2-ethylhexyl) phthalate-degrading enrichment culture. The final genome assembly consists of a 5.10-Mbp chromosome and a plasmid (159 kbp). A total of 4,814 coding sequences were predicted, including 4,741 protein-coding sequences. We report the complete genome sequence of Gordonia rubripertincta SD5, isolated from a soil-derived di-(2-ethylhexyl) phthalate-degrading enrichment culture. The final genome assembly consists of a 5.10-Mbp chromosome and a plasmid (159 kbp). A total of 4,814 coding sequences were predicted, including 4,741 protein-coding sequences.
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Bottos EM, Al-Shabib EY, Shaw DMJ, McAmmond BM, Sharma A, Suchan DM, Cameron ADS, Van Hamme JD. Transcriptomic response of Gordonia sp. strain NB4-1Y when provided with 6:2 fluorotelomer sulfonamidoalkyl betaine or 6:2 fluorotelomer sulfonate as sole sulfur source. Biodegradation 2020; 31:407-422. [PMID: 33150552 PMCID: PMC7661421 DOI: 10.1007/s10532-020-09917-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/27/2020] [Indexed: 02/06/2023]
Abstract
Abstract Perfluoroalkyl and polyfluoroalkyl substances (PFAS) are environmental contaminants of concern. We previously described biodegradation of two PFAS that represent components and transformation products of aqueous film-forming foams (AFFF), 6:2 fluorotelomer sulfonamidoalkyl betaine (6:2 FTAB) and 6:2 fluorotelomer sulfonate (6:2 FTSA), by Gordonia sp. strain NB4-1Y. To identify genes involved in the breakdown of these compounds, the transcriptomic response of NB4-1Y was examined when grown on 6:2 FTAB, 6:2 FTSA, a non-fluorinated analog of 6:2 FTSA (1-octanesulfonate), or MgSO4, as sole sulfur source. Differentially expressed genes were identified as those with ± 1.5 log2-fold-differences (± 1.5 log2FD) in transcript abundances in pairwise comparisons. Transcriptomes of cells grown on 6:2 FTAB and 6:2 FTSA were most similar (7.9% of genes expressed ± 1.5 log2FD); however, several genes that were expressed in greater abundance in 6:2 FTAB treated cells compared to 6:2 FTSA treated cells were noted for their potential role in carbon–nitrogen bond cleavage in 6:2 FTAB. Responses to sulfur limitation were observed in 6:2 FTAB, 6:2 FTSA, and 1-octanesulfonate treatments, as 20 genes relating to global sulfate stress response were more highly expressed under these conditions compared to the MgSO4 treatment. More highly expressed oxygenase genes in 6:2 FTAB, 6:2 FTSA, and 1-octanesulfonate treatments were found to code for proteins with lower percent sulfur-containing amino acids compared to both the total proteome and to oxygenases showing decreased expression. This work identifies genetic targets for further characterization and will inform studies aimed at evaluating the biodegradation potential of environmental samples through applied genomics. Graphic Abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s10532-020-09917-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eric M Bottos
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada
| | - Ebtihal Y Al-Shabib
- Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
- Faculty of Science, Institute for Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Dayton M J Shaw
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada
| | - Breanne M McAmmond
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada
| | - Aditi Sharma
- Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
- Faculty of Science, Institute for Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Danae M Suchan
- Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
- Faculty of Science, Institute for Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Andrew D S Cameron
- Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
- Faculty of Science, Institute for Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Jonathan D Van Hamme
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada.
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Seasonal Dynamics of the Activated Sludge Microbiome in Sequencing Batch Reactors, Assessed Using 16S rRNA Transcript Amplicon Sequencing. Appl Environ Microbiol 2020; 86:AEM.00597-20. [PMID: 32709723 DOI: 10.1128/aem.00597-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/17/2020] [Indexed: 12/29/2022] Open
Abstract
Activated sludge is comprised of diverse microorganisms which remediate wastewater. Previous research has characterized activated sludge using 16S rRNA gene amplicon sequencing, which can help to address questions on the relative abundance of microorganisms. In this study, we used 16S rRNA transcript sequencing in order to characterize "active" populations (via protein synthesis potential) and gain a deeper understanding of microbial activity patterns within activated sludge. Seasonal abundances of individual populations in activated sludge change over time, yet a persistent group of core microorganisms remains throughout the year which are traditionally classified on presence or absence without monitoring of their activity or growth. The goal of this study was to further our understanding of how the activated sludge microbiome changes between seasons with respect to population abundance, activity, and growth. Triplicate sequencing batch reactors were sampled at 10-min intervals throughout reaction cycles during all four seasons. We quantified the gene and transcript copy numbers of 16S rRNA amplicons using real-time PCR and sequenced the products to reveal community abundance and activity changes. We identified 108 operational taxonomic units (OTUs) with stable abundance, activity, and growth throughout the year. Nonproliferating OTUs were commonly human health related, while OTUs that showed seasonal abundance changes have previously been identified as being associated with floc formation and bulking. We observed significant differences in 16S rRNA transcript copy numbers, particularly at lower temperatures in winter and spring. The study provides an analysis of the seasonal dynamics of microbial activity variations in activated sludge based on quantifying and sequencing 16S rRNA transcripts.IMPORTANCE Sequencing batch reactors are a common design for wastewater treatment plants, particularly in smaller municipalities, due to their low footprint and ease of operations. However, like for most treatment plants in temperate/continental climates, the microbial community involved in water treatment is highly seasonal and its biological processes can be sensitive to cold temperatures. The seasonality of these microbial communities has been explored primarily in conventional treatment plants and not in sequencing batch reactors. Furthermore, most studies often only address which organisms are present. However, the activated sludge microbial community is very diverse, and it is often hard to discern which organisms are active and which organisms are simply present. In this study, we applied additional sequencing techniques to also address the issues of which organisms are active and which organisms are growing. By addressing these issues, we gained new insights into seasonal microbial populations dynamics and activity patterns affecting wastewater treatment.
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Nguyen LH, Nguyen HD, Tran PT, Nghiem TT, Nguyen TT, Dao VL, Phan TN, To AK, Hatamoto M, Yamaguchi T, Kasai D, Fukuda M. Biodegradation of natural rubber and deproteinized natural rubber by enrichment bacterial consortia. Biodegradation 2020; 31:303-317. [PMID: 32914250 DOI: 10.1007/s10532-020-09911-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/05/2020] [Indexed: 11/28/2022]
Abstract
This study examined the biodegradation of natural rubber (NR) and deproteinized natural rubber (DPNR) by bacterial consortia enriched from a rubber-processing factory's waste in Vietnam. The results reveal the degradation in both NR and DPNR, and the DPNR was degraded easier than NR. The highest weight loss of 48.37% was obtained in the fourth enrichment consortium with DPNR, while 35.39% was obtained in the fifth enrichment consortium with NR after 14 days of incubation. Nitrogen content and fatty acid content determined by Kjeldahl method and fourier transform infrared spectroscopy (FTIR), respectively, were decreased significantly after being incubated with the consortia. Structure of degraded rubber film analyzed by nuclear magnetic resonance spectroscopy showed the presence of aldehyde group, a sign of rubber degradation. Bacterial cells tightly adhering and embedding into NR and DPNR films were observed by scanning electron microscopy. There were differences in the bacterial composition of the consortia with NR and DPNR, which were determined by metagenomic analysis using 16S rRNA gene sequencing. The phyla Bacteroidetes and Proteobacteria may play a role in the degradation of non-isoprene compounds such as protein or lipid, while the phylum Actinobacteria plays a crucial role in the degradation of rubber hydrocarbon in all consortia.
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Affiliation(s)
- Lan Huong Nguyen
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, No 1, Dai Co Viet street, Hanoi, Vietnam.
| | - Hoang Dung Nguyen
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, No 1, Dai Co Viet street, Hanoi, Vietnam
| | - P Thao Tran
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Japan
| | - Thi Thuong Nghiem
- School of Chemical Engineering, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - Thi Thanh Nguyen
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, No 1, Dai Co Viet street, Hanoi, Vietnam
| | - Viet Linh Dao
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, No 1, Dai Co Viet street, Hanoi, Vietnam.,Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Trung Nghia Phan
- School of Chemical Engineering, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - Anh Kim To
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, No 1, Dai Co Viet street, Hanoi, Vietnam
| | - Masashi Hatamoto
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Japan
| | - Daisuke Kasai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Masao Fukuda
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan.,Department of Biological Chemistry, Chubu University, Kasugai, Japan
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