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Sachdeva S, Sarethy IP. Diving into freshwater microbial metabolites: Pioneering research and future prospects. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024:1-19. [PMID: 38887995 DOI: 10.1080/09603123.2024.2351153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 04/30/2024] [Indexed: 06/20/2024]
Abstract
In practically every facet of life, especially nutrition, agriculture, and healthcare, microorganisms offer a prospective origin for abundant natural substances and products. Among these microorganisms, bacteria also possess the capability to rapidly acclimate to diverse environments, utilize varied resources, and effectively respond to environmental fluctuations, including those influenced by human activities like pollution and climate change. The ever-changing environment of freshwater bodies influences bacterial communities, offering opportunities for improving health and environmental conservation that remain unexplored. Herein, the study discusses the bacterial taxa along with specialised metabolites with antioxidant, antibacterial, and anticancer activity that have been identified from freshwater environments, thus achieving Sustainable Development Goals addressing health and wellbeing (SDG-3), economic growth (SDG-8) along with industrial development (SDG-9). The present review is intended as a compendium for research teams working in the fields of medicinal chemistry, organic chemistry, clinical research, and natural product chemistry.
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Affiliation(s)
- Saloni Sachdeva
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Indira P Sarethy
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
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Ma Y, Guo P, Chen X, Xu M, Liu W, Jin X. Anti-Klebsiella pneumoniae activity of secondary metabolism of Achromobacter from the intestine of Periplaneta americana. BMC Microbiol 2023; 23:162. [PMID: 37277707 DOI: 10.1186/s12866-023-02909-7] [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: 08/12/2022] [Accepted: 05/25/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae is one of the main pathogens of clinical isolation and nosocomial infections, as K. pneumoniae show broad-spectrum resistance to β-lactam and carbapenem antibiotics. It is emerging clinical need for a safe and effective drug to anti-K. pneumoniae. At present, Achromobacter mainly focused on its degradation of petroleum hydrocarbons, polycyclic aromatic hydrocarbons, assisting insects to decompose, degrade heavy metals and utilize organic matter, but there were few reports on the antibacterial activity of the secondary metabolites of Achromobacter. RESULTS In this study, a strain WA5-4-31 from the intestinal tract of Periplaneta americana exhibited strong activity against K. Pneumoniae through preliminary screening. The strain was determined to be Achromobacter sp. through the morphological characteristics, genotyping and phylogenetic tree analysis, which is homologous to Achromobacter ruhlandii by 99%, its accession numbe in GenBank at National Center for Biotechnology Information (NCBI) is MN007235, and its deposit number was GDMCC NO.1.2520. Six compounds (Actinomycin D, Actinomycin X2, Collismycin A, Citrinin, Neoechinulin A and Cytochalasin E) were isolated and determined by activity tracking, chemical separation, nuclear magnetic resonance (NMR) and mass spectrometry (MS) analysis. Among them, Actinomycin D, Actinomycin X2, Collismycin A, Citrinin and Cytochalasin E showed a good effect on anti-K. pneumoniae, with MIC values of 16-64 µg/mL. CONCLUSIONS The study reported Achromobacter, which was from the intestinal tract of Periplaneta americana with the activity against K. Pneumoniae, can produce antibacterial compounds for the first time. It lays the foundation for development of secondary metabolites of insect intestinal microorganisms.
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Affiliation(s)
- Yan Ma
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Ping Guo
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, China
- Clinical Laboratory, Shenzhen Bao'An District Central Hospital, Shenzhen, 518103, China
| | - Xueqin Chen
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Minhua Xu
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, China
- Clinical laboratory, Foshan Fosun Chancheng Hospital, Foshan, 528000, China
| | - Wenbin Liu
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Xiaobao Jin
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
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Rolbiecki D, Korzeniewska E, Czatzkowska M, Harnisz M. The Impact of Chlorine Disinfection of Hospital Wastewater on Clonal Similarity and ESBL-Production in Selected Bacteria of the Family Enterobacteriaceae. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:13868. [PMID: 36360746 PMCID: PMC9655713 DOI: 10.3390/ijerph192113868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/21/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Hospitals are regarded as ecological niches of antibiotic-resistant bacteria (ARB). ARB can spread outside the hospital environment via hospital wastewater (HWW). Therefore, HWW is often disinfected in local stations to minimize that risk. Chlorine-based treatment is the most popular method of HWW disinfection around the world, however, recent research has suggested that it can contribute to the spread of antimicrobial resistance (AMR). The aim of this study is to determine the impact of HWW disinfection on the clonal similarity of Enterobacteriaceae species and their ability to produce extended-spectrum beta-lactamases (ESBLs). The study was conducted in a hospital with a local chlorine-based disinfection station. Samples of wastewater before disinfection and samples of disinfected wastewater, collected in four research seasons, were analyzed. Bacteria potentially belonging to the Enterobacteriaceae family were isolated from HWW. The Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) method was used to generate DNA fingerprints of all bacterial isolates. The isolates were phenotypically tested for the production of ESBLs. Antibiotic resistance genes (blaSHV, blaTEM, and blaOXA, blaCTX-M-1-group, blaCTX-M-2-group, blaCTX-9-group and blaCTX-M-8/25-group) were detected by PCR in strains with confirmed phenotypic ability to produce ESBLs. The ESBL+ isolates were identified by the sequencing of 16S rDNA. In the present study, the same bacterial clones were isolated from HWW before and after disinfection and HWW was sampled in different seasons. Genetic and phenotypic variations were observed in bacterial clones. ESBL+ strains were isolated significantly more often from disinfected than from non-disinfected HWW. The blaOXA gene was significantly more prevalent in isolates from disinfected than non-disinfected HWW. Enterobacter hormaechei and Klebsiella pneumoniae were the dominant species in ESBL+ strains isolated from both sampling sites. The results of this study indicate that chlorine-based disinfection promotes the survival of ESBL-producing bacteria and/or the transmission of genetic determinants of antimicrobial resistance. As a result, chlorination increases the proportion of ESBL-producing Enterobacteriaceae in disinfected wastewater. Consequently, chlorine-based disinfection practices may pose a risk to the environment and public health by accelerating the spread of antimicrobial resistance.
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Zhao Y, Gao J, Wang Z, Cui Y, Zhang Y, Dai H, Li D. Distinct bacterial communities and resistance genes enriched by triclocarban-contaminated polyethylene microplastics in antibiotics and heavy metals polluted sewage environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 839:156330. [PMID: 35640752 DOI: 10.1016/j.scitotenv.2022.156330] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Knowledge gaps still surround the question of what biofilms form on contaminated microplastics (MPs) in the antibiotics and (or) heavy metals polluted sewage. In this work, the clean polyethylene microplastics (PE MPs) and triclocarban (TCC)-contaminated PE MPs were cultured in the sewage containing only ampicillin (AMP), only copper (Cu) and both AMP and Cu for 28 days. The results showed that the TCC on PE MPs (with concentration of 2.48 mg/g PE MPs) did not impede the adhesion of the bacteria and the formation of biofilm. Moreover, many potential pathogenic bacteria (Aquabacterium and Pseudoxanthomonas) and potential resistant bacteria (Stenotrophomonas) were more likely to attach on TCC-contaminated PE MPs compared with clean PE MPs. In addition, biofilms of TCC-contaminated PE MPs had highest potential pathogenic functions. TCC-contaminated PE MPs also caused the increases of various resistance genes in both biofilm and sewage. The co-occurrence of TCC, AMP and Cu might exert a stronger selective pressure on bacterial communities and promote the co-selection of resistance genes. In addition, TCC-contaminated PE MPs resulted in higher abundance of five mobile genetic elements (MGEs) (intI1, intI3, tnpA-04, IS613 and trb-C) in sewage, which might further promote the transmission of resistance genes.
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Affiliation(s)
- Yifan Zhao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Jingfeng Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China.
| | - Zhiqi Wang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Yingchao Cui
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Yi Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Huihui Dai
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Dingchang Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
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Tenebro CP, Trono DJVL, Vicera CVB, Sabido EM, Ysulat JA, Macaspac AJM, Tampus KA, Fabrigar TAP, Saludes JP, Dalisay DS. Multiple strain analysis of Streptomyces species from Philippine marine sediments reveals intraspecies heterogeneity in antibiotic activities. Sci Rep 2021; 11:17544. [PMID: 34475427 PMCID: PMC8413401 DOI: 10.1038/s41598-021-96886-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/10/2021] [Indexed: 12/17/2022] Open
Abstract
The marine ecosystem has become the hotspot for finding antibiotic-producing actinomycetes across the globe. Although marine-derived actinomycetes display strain-level genomic and chemodiversity, it is unclear whether functional traits, i.e., antibiotic activity, vary in near-identical Streptomyces species. Here, we report culture-dependent isolation, antibiotic activity, phylogeny, biodiversity, abundance, and distribution of Streptomyces isolated from marine sediments across the west-central Philippines. Out of 2212 marine sediment-derived actinomycete strains isolated from 11 geographical sites, 92 strains exhibited antibacterial activities against multidrug-resistant Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli. The 16S rRNA and rpoB gene sequence analyses confirmed that antibiotic-producing strains belong to the genus Streptomyces, highlighting Streptomyces parvulus as the most dominant species and three possible new species. Antibiotic-producing Streptomyces strains were highly diverse in Southern Antique, and species diversity increase with marine sediment depth. Multiple strains with near-identical 16S rRNA and rpoB gene sequences displayed varying strength of antibiotic activities. The genotyping of PKS and NRPS genes revealed that closely related antibiotic-producing strains have similar BGC domains supported by their close phylogenetic proximity. These findings collectively suggest Streptomyces' intraspecies adaptive characteristics in distinct ecological niches that resulted in outcompeting other bacteria through differential antibiotic production.
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Affiliation(s)
- Chuckcris P Tenebro
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, 5000, Iloilo City, Philippines
| | - Dana Joanne Von L Trono
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, 5000, Iloilo City, Philippines
| | - Carmela Vannette B Vicera
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, 5000, Iloilo City, Philippines
| | - Edna M Sabido
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, 5000, Iloilo City, Philippines
| | - Jovito A Ysulat
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, 5000, Iloilo City, Philippines
| | - Aaron Joseph M Macaspac
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, 5000, Iloilo City, Philippines
| | - Kimberly A Tampus
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, 5000, Iloilo City, Philippines
| | - Trisha Alexis P Fabrigar
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, 5000, Iloilo City, Philippines
| | - Jonel P Saludes
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, 5000, Iloilo City, Philippines.,Department of Chemistry, College of Liberal Arts, Sciences, and Education, University of San Agustin, 5000, Iloilo City, Philippines.,Balik Scientist Program, Department of Science and Technology, Philippine Council for Health Research and Development (PCHRD), 1631, Bicutan, Taguig City, Philippines
| | - Doralyn S Dalisay
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, 5000, Iloilo City, Philippines. .,Department of Biology, College of Liberal Arts, Sciences, and Education, University of San Agustin, 5000, Iloilo City, Philippines. .,Balik Scientist Program, Department of Science and Technology, Philippine Council for Health Research and Development (PCHRD), 1631, Bicutan, Taguig City, Philippines.
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Sabido EM, Tenebro CP, Trono DJVL, Vicera CVB, Leonida SFL, Maybay JJWB, Reyes-Salarda R, Amago DS, Aguadera AMV, Octaviano MC, Saludes JP, Dalisay DS. Insights into the Variation in Bioactivities of Closely Related Streptomyces Strains from Marine Sediments of the Visayan Sea against ESKAPE and Ovarian Cancer. Mar Drugs 2021; 19:md19080441. [PMID: 34436280 PMCID: PMC8399204 DOI: 10.3390/md19080441] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/27/2021] [Accepted: 07/27/2021] [Indexed: 12/25/2022] Open
Abstract
Marine sediments host diverse actinomycetes that serve as a source of new natural products to combat infectious diseases and cancer. Here, we report the biodiversity, bioactivities against ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) and ovarian cancer, and metabolites variation among culturable actinomycetes isolated from the marine sediments of Visayan Sea, Philippines. We identified 15 Streptomyces species based on a 16S rRNA gene sequence analysis. The crude extracts of 10 Streptomyces species have inhibited the growth of ESKAPE pathogens with minimum inhibitory concentration (MIC) values ranging from 0.312 mg/mL to 20 mg/mL depending on the strain and pathogens targeted. Additionally, ten crude extracts have antiproliferative activity against A2780 human ovarian carcinoma at 2 mg/mL. To highlight, we observed that four phylogenetically identical Streptomyces albogriseolus strains demonstrated variation in antibiotic and anticancer activities. These strains harbored type I and II polyketide synthase (PKS) and non-ribosomal synthetase (NRPS) genes in their genomes, implying that their bioactivity is independent of the polymerase chain reaction (PCR)-detected bio-synthetic gene clusters (BGCs) in this study. Metabolite profiling revealed that the taxonomically identical strains produced core and strain-specific metabolites. Thus, the chemical diversity among these strains influences the variation observed in their biological activities. This study expanded our knowledge on the potential of marine-derived Streptomyces residing from the unexplored regions of the Visayan Sea as a source of small molecules against ESKAPE pathogens and cancer. It also highlights that Streptomyces species strains produce unique strain-specific secondary metabolites; thus, offering new chemical space for natural product discovery.
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Affiliation(s)
- Edna M. Sabido
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, Iloilo City 5000, Philippines; (E.M.S.); (S.F.L.L.); (J.J.W.B.M.); (D.S.A.); (A.M.V.A.); (M.C.O.)
| | - Chuckcris P. Tenebro
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, Iloilo City 5000, Philippines; (C.P.T.); (D.J.V.L.T.); (C.V.B.V.); (R.R.-S.)
| | - Dana Joanne Von L. Trono
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, Iloilo City 5000, Philippines; (C.P.T.); (D.J.V.L.T.); (C.V.B.V.); (R.R.-S.)
| | - Carmela Vannette B. Vicera
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, Iloilo City 5000, Philippines; (C.P.T.); (D.J.V.L.T.); (C.V.B.V.); (R.R.-S.)
| | - Sheeny Fane L. Leonida
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, Iloilo City 5000, Philippines; (E.M.S.); (S.F.L.L.); (J.J.W.B.M.); (D.S.A.); (A.M.V.A.); (M.C.O.)
| | - Jose Jeffrey Wayne B. Maybay
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, Iloilo City 5000, Philippines; (E.M.S.); (S.F.L.L.); (J.J.W.B.M.); (D.S.A.); (A.M.V.A.); (M.C.O.)
| | - Rikka Reyes-Salarda
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, Iloilo City 5000, Philippines; (C.P.T.); (D.J.V.L.T.); (C.V.B.V.); (R.R.-S.)
- Department of Biology, College of Liberal Arts, Sciences, and Education, University of San Agustin, Iloilo City 5000, Philippines
| | - Diana S. Amago
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, Iloilo City 5000, Philippines; (E.M.S.); (S.F.L.L.); (J.J.W.B.M.); (D.S.A.); (A.M.V.A.); (M.C.O.)
| | - Angelica Marie V. Aguadera
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, Iloilo City 5000, Philippines; (E.M.S.); (S.F.L.L.); (J.J.W.B.M.); (D.S.A.); (A.M.V.A.); (M.C.O.)
| | - May C. Octaviano
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, Iloilo City 5000, Philippines; (E.M.S.); (S.F.L.L.); (J.J.W.B.M.); (D.S.A.); (A.M.V.A.); (M.C.O.)
| | - Jonel P. Saludes
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, Iloilo City 5000, Philippines; (E.M.S.); (S.F.L.L.); (J.J.W.B.M.); (D.S.A.); (A.M.V.A.); (M.C.O.)
- Department of Chemistry, College of Liberal Arts, Sciences, and Education, University of San Agustin, Iloilo City 5000, Philippines
- Tuklas Lunas Development Center, University of San Agustin, Iloilo City 5000, Philippines
- Balik Scientist Program, Department of Science and Technology, Philippine Council for Health Research and Development (PCHRD), Bicutan, Taguig City 1631, Philippines
- Correspondence: (J.P.S.); (D.S.D.); Tel.: +63-33-503-6887 (J.P.S.); +63-33-501-0350 (D.S.D.)
| | - Doralyn S. Dalisay
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, Iloilo City 5000, Philippines; (C.P.T.); (D.J.V.L.T.); (C.V.B.V.); (R.R.-S.)
- Department of Biology, College of Liberal Arts, Sciences, and Education, University of San Agustin, Iloilo City 5000, Philippines
- Tuklas Lunas Development Center, University of San Agustin, Iloilo City 5000, Philippines
- Balik Scientist Program, Department of Science and Technology, Philippine Council for Health Research and Development (PCHRD), Bicutan, Taguig City 1631, Philippines
- Correspondence: (J.P.S.); (D.S.D.); Tel.: +63-33-503-6887 (J.P.S.); +63-33-501-0350 (D.S.D.)
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Suarez AFL, Tirador ADG, Villorente ZM, Bagarinao CF, Sollesta JVN, Dumancas GG, Sun Z, Zhan ZQ, Saludes JP, Dalisay DS. The Isorhamnetin-Containing Fraction of Philippine Honey Produced by the Stingless Bee Tetragonula biroi Is an Antibiotic against Multidrug-Resistant Staphylococcus aureus. Molecules 2021; 26:1688. [PMID: 33802916 PMCID: PMC8002709 DOI: 10.3390/molecules26061688] [Citation(s) in RCA: 3] [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: 01/18/2021] [Revised: 02/26/2021] [Accepted: 03/05/2021] [Indexed: 12/27/2022] Open
Abstract
Honey exhibits antibacterial and antioxidant activities that are ascribed to its diverse secondary metabolites. In the Philippines, the antibacterial and antioxidant activities, as well as the bioactive metabolite contents of the honey, have not been thoroughly described. In this report, we investigated the in vitro antibacterial and antioxidant activities of honey from Apis mellifera and Tetragonula biroi, identified the compound responsible for the antibacterial activity, and compared the observed bioactivities and metabolite profiles to that of Manuka honey, which is recognized for its antibacterial and antioxidant properties. The secondary metabolite contents of honey were extracted using a nonionic polymeric resin followed by antibacterial and antioxidant assays, and then spectroscopic analyses of the phenolic and flavonoid contents. Results showed that honey extracts produced by T. biroi exhibits antibiotic activity against Staphylococcal pathogens as well as high antioxidant activity, which are correlated to its high flavonoid and phenolic content as compared to honey produced by A. mellifera. The bioassay-guided fractionation paired with Liquid Chromatography Mass Spectrometry (LCMS) and tandem MS analyses found the presence of the flavonoid isorhamnetin (3-methylquercetin) in T. biroi honey extract, which was demonstrated as one of the compounds with inhibitory activity against multidrug-resistant Staphylococcus aureus ATCC BAA-44. Our findings suggest that Philippine honey produced by T. biroi is a potential nutraceutical that possesses antibiotic and antioxidant activities.
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Affiliation(s)
- Angelica Faith L. Suarez
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, Iloilo City 5000, Philippines; (A.F.L.S.); (A.D.G.T.)
| | - April Dawn G. Tirador
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, Iloilo City 5000, Philippines; (A.F.L.S.); (A.D.G.T.)
| | - Zenith M. Villorente
- Maridan Industries, Inc., Jaro, Iloilo City 5000, Philippines; (Z.M.V.); (C.F.B.); (J.V.N.S.)
| | - Cathrina F. Bagarinao
- Maridan Industries, Inc., Jaro, Iloilo City 5000, Philippines; (Z.M.V.); (C.F.B.); (J.V.N.S.)
| | - Jan Vincent N. Sollesta
- Maridan Industries, Inc., Jaro, Iloilo City 5000, Philippines; (Z.M.V.); (C.F.B.); (J.V.N.S.)
| | - Gerard G. Dumancas
- Department of Mathematics and Physical Sciences, Louisiana State University at Alexandria, Alexandria, LA 71302, USA;
- Balik Scientist Program, Philippine Council for Health Research and Development (PCHRD), Department of Science and Technology, Bicutan, Taguig City 1631, Philippines;
| | - Zhe Sun
- Shimadzu Asia Pacific (SAP), Singapore Science Park I, Singapore 118264, Singapore; (Z.S.); (Z.Q.Z.)
| | - Zhao Qi Zhan
- Shimadzu Asia Pacific (SAP), Singapore Science Park I, Singapore 118264, Singapore; (Z.S.); (Z.Q.Z.)
| | - Jonel P. Saludes
- Balik Scientist Program, Philippine Council for Health Research and Development (PCHRD), Department of Science and Technology, Bicutan, Taguig City 1631, Philippines;
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, Iloilo City 5000, Philippines
- Department of Chemistry, College of Liberal Arts, Sciences, and Education, University of San Agustin, Iloilo City 5000, Philippines
| | - Doralyn S. Dalisay
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, Iloilo City 5000, Philippines; (A.F.L.S.); (A.D.G.T.)
- Balik Scientist Program, Philippine Council for Health Research and Development (PCHRD), Department of Science and Technology, Bicutan, Taguig City 1631, Philippines;
- Department of Biology, College of Liberal Arts, Sciences, and Education, University of San Agustin, Iloilo City 5000, Philippines
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Antimicrobial activity of Actinobacteria isolated from dry land soil in Yazd, Iran. Mol Biol Rep 2021; 48:1717-1723. [PMID: 33599952 DOI: 10.1007/s11033-021-06218-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/06/2021] [Indexed: 10/22/2022]
Abstract
Historically, many important secondary metabolites including antibiotics used in clinic are purified from the cultural broths of Actinobacteria, which were inhabited in soil. Yazd is located in the center of Iran, the south of the Dasht-e Kavir and the west of the Dasht-e Lut; accordingly it has a hot, dry climate with long summers. In the present study, 18 strains of Actinobacteria isolated from 60 soil samples from Yazd-Iran. Pure isolates were screened for antibacterial activity against the ATCC strains by using two methods: single line streak method and spot inoculation method. ATCC strains include four antibiotic resistant ATCC strains (Enterococcus faecalis, Staphylococcus aureus, Klebsiella pneumoniae and, Acinetobacter baumannii) and three antibiotic sensitive strains (Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli) and, Bacillus subtilis. Seven isolates exhibited antimicrobial activity against the ATCC strains (38.8%). Identification of type I and type II polyketide synthases (pksI, pksII) and nonribosomal peptide synthetase (NRPS) genes were done for these 7 isolates and all of 7 strains, possessed at least one of these genes. The results of this study confirm that soil Actinobacteria bear a great ability to produce antibacterial compounds against resistant and sensitive test organisms.
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Antimicrobial sensitivity profiling of bacterial communities recovered from effluents of municipal solid waste dumping site. 3 Biotech 2021; 11:37. [PMID: 33479592 DOI: 10.1007/s13205-020-02548-z] [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: 07/26/2020] [Accepted: 11/06/2020] [Indexed: 10/22/2022] Open
Abstract
The diversity of antibiotic-resistance bacteria (ARB) from the effluents of Aizawl city municipal waste dumping site was studied using a culture-dependent method. The present study molecularly identified 73 isolates that were differentiated into three phyla (Proteobacteria, Actinobacteria, and Firmicutes) belonging to 17 family and 22 genera. Bacillus constitutes the most dominant genus comprising 16% of the total isolates. The topology of the phylogenetic tree differentiates them into five major clades. Corynebacterium and Rhodococcus which are morphologically alike were clustered together and the Gram-positive bacteria such as Staphylococcus, Bacillus, and Lysinibacillus formed a separate cluster. Antibiotic resistance of the identified bacterial isolates was performed using 19 different antibiotics. Among the isolates, 70 of them found resistant to polymixin B and nalidixic acid and 10 isolates exhibited resistance to 15 tested antibiotics. The present study revealed that bacteria with antibiotic resistance are extensively distributed in the effluents of the dumping site and may serve as a significant reservoir for the spreading of antibiotic resistance to opportunistic pathogens.
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10
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Zhao Y, Gao J, Wang Z, Dai H, Wang Y. Responses of bacterial communities and resistance genes on microplastics to antibiotics and heavy metals in sewage environment. JOURNAL OF HAZARDOUS MATERIALS 2021; 402:123550. [PMID: 33254740 DOI: 10.1016/j.jhazmat.2020.123550] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/14/2020] [Accepted: 07/21/2020] [Indexed: 05/11/2023]
Abstract
In present study, copper (Cu), zinc (Zn), tetracycline (TC) and ampicillin (AMP) were selected to study the individual and synergistic effects of antibiotics and heavy metals on the microbial communities and resistance genes on polyvinyl chloride microplastics (PVC MPs) and surrounding sewage after 28 and 84 days. The results indicated that PVC MPs enriched many microorganisms from surrounding sewage, especially pathogenic bacteria such as Mycobacterium and Aquabacterium. The resistance gene with the highest abundance enriched on PVC MPs was tnpA (average abundance of 1.0 × 107 copies/mL sewage). The single presence of Zn, TC and AMP inhibited these enrichments for a short period of time (28 days). But the single presence of Cu and the co-existence of antibiotics and heavy metals inhibited these enrichments for a long period of time (84 days), resulting in relatively low microbial diversities and resistance genes abundances. Transpose tnpA had significantly positive correlations (p < 0.05) with all other genes. Pathogenic bacteria Mycobacterium and Legionella were potential hosts harboring 5 and 1 resistance genes, respectively. Overall, PVC MPs played important roles in the distribution and transfer of pathogenic bacteria and resistance genes in sewage with the presence of antibiotics or (and) heavy metals.
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Affiliation(s)
- Yifan Zhao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Jingfeng Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China.
| | - Zhiqi Wang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Huihui Dai
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Yuwei Wang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
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11
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Marine Sediment-Derived Streptomyces Strain Produces Angucycline Antibiotics against Multidrug-Resistant Staphylococcus aureus Harboring SCCmec Type 1 Gene. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2020. [DOI: 10.3390/jmse8100734] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Philippine archipelago is geographically positioned in the tropics with rich areas of marine biodiversity. Its marine sediments harbor actinomycetes that exhibit antibacterial activity. Screening of actinomycetes isolated from marine sediments collected near the coast of Islas de Gigantes, Iloilo showed one isolate that exhibited high activity against the multidrug-resistant Staphylococcus aureus (MRSA) strain carrying the Staphylococcal Cassette Chromosome mec (SCCmec) type 1 gene, a biomarker for drug resistance. The isolate was identified as Streptomyces sp. strain DSD011 based on its 16s rRNA and protein-coding genes (atpD, recA, rpoB, and trpB) sequences, and was found to be a new species of salt-tolerant marine Streptomyces. Further, the strain harbors both non-ribosomal peptide synthetase (NRPS) and type II polyketide synthase (PKS) in its genome. The targeted chromatographic isolation and chemical investigations by Liquid Chromatography Mass Spectrometry-Time of Flight (LCMS-TOF), tandem mass spectrometry (MS/MS), and Global Natural Product Social molecular networking (GNPS) of the antibiotics produced by the strain afforded the two polycyclic aromatic polyketide angucycline glycosides, fridamycin A (1) and fridamycin D (2), which are products of type II PKS biosynthesis. Compounds 1 and 2 displayed antibacterial activity against MRSA with minimum inhibitory concentration (MIC) of 500 μg/mL and 62.5 μg/mL, respectively. These results suggest that the underexplored marine sediments near the coast of Islas de Gigantes, Iloilo offer access to undiscovered Streptomyces species that are invaluable sources of antibiotic leads.
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12
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Limbu SM, Zhang H, Luo Y, Chen LQ, Zhang M, Du ZY. High carbohydrate diet partially protects Nile tilapia (Oreochromis niloticus) from oxytetracycline-induced side effects. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 256:113508. [PMID: 31706777 DOI: 10.1016/j.envpol.2019.113508] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 09/08/2019] [Accepted: 10/27/2019] [Indexed: 06/10/2023]
Abstract
Antibiotics used in global aquaculture production cause various side effects, which impair fish health. However, the use of dietary composition such as carbohydrate, which is one of the dominant components in fish diets to attenuate the side effects induced by antibiotics, remains unclear. We determined the ability of high carbohydrate diet to protect Nile tilapia (Oreochromis niloticus) from oxytetracycline-induced side effects. Triplicate groups of thirty O. niloticus (9.50 ± 0.08 g) were fed on medium carbohydrate (MC; 335 g/kg) and high carbohydrate (HC; 455 g/kg) diets without and with 2.00 g/kg diet of oxytetracycline (80 mg/kg body weight/day) hereafter, MCO and HCO for 35 days. Thereafter, we assessed growth performance, hepatic nutrients composition and metabolism, microbiota abundance, immunity, oxidative and cellular stress, hepatotoxicity, lipid peroxidation and apoptosis. To understand the possible mechanism of carbohydrate protection on oxytetracycline, we assessed the binding effects and efficiencies of mixtures of medium and high starch with oxytetracycline as well as the MCO and HCO diets. The O. niloticus fed on the MCO and HCO diets had lower growth rate, nutrients utilization and survival rate than those fed on the MC and HC diets, respectively. Dietary HCO increased hepatosomatic index and hepatic protein content of O. niloticus than MCO diet. The O. niloticus fed on the HCO diet had lower mRNA expression of genes related to protein, glycogen and lipid metabolism compared to those fed on the MCO diet. Feeding O. niloticus on the HCO diet increased innate immunity and reduced pathogenic bacteria, pro-inflammation, hepatotoxicity, cellular stress and apoptosis than the MCO diet. The high starch with oxytetracycline and HCO diet had higher-oxytetracycline binding effects and efficiencies than the medium starch with oxytetracyline and MCO diet, respectively. Our study demonstrates that, high carbohydrate partially protects O. niloticus from oxytetracycline-induced side effects by binding the antibiotic. Incorporating high carbohydrate in diet formulation for omnivorous fish species alleviates some of the side effects caused by antibiotics.
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Affiliation(s)
- Samwel Mchele Limbu
- Laboratory of Aquaculture Nutrition Environmental Health (LANEH), School of Life Sciences, East China Normal University, 500 Dongchuan Rd, Shanghai, 200241, China; Department of Aquatic Sciences and Fisheries Technology, University of Dar es Salaam, P.O. Box 35064, Dar es Salaam, Tanzania
| | - Han Zhang
- Laboratory of Aquaculture Nutrition Environmental Health (LANEH), School of Life Sciences, East China Normal University, 500 Dongchuan Rd, Shanghai, 200241, China
| | - Yuan Luo
- Laboratory of Aquaculture Nutrition Environmental Health (LANEH), School of Life Sciences, East China Normal University, 500 Dongchuan Rd, Shanghai, 200241, China
| | - Li-Qiao Chen
- Laboratory of Aquaculture Nutrition Environmental Health (LANEH), School of Life Sciences, East China Normal University, 500 Dongchuan Rd, Shanghai, 200241, China
| | - Meiling Zhang
- Laboratory of Aquaculture Nutrition Environmental Health (LANEH), School of Life Sciences, East China Normal University, 500 Dongchuan Rd, Shanghai, 200241, China
| | - Zhen-Yu Du
- Laboratory of Aquaculture Nutrition Environmental Health (LANEH), School of Life Sciences, East China Normal University, 500 Dongchuan Rd, Shanghai, 200241, China.
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13
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Chen X, Fang S, Wei L, Zhong Q. Systematic evaluation of the gut microbiome of swamp eel ( Monopterus albus) by 16S rRNA gene sequencing. PeerJ 2019; 7:e8176. [PMID: 31875148 PMCID: PMC6927349 DOI: 10.7717/peerj.8176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 11/07/2019] [Indexed: 12/11/2022] Open
Abstract
Background The swamp eel (Monopterus albus) is a commercially important farmed species in China. The dysbiosis and homeostasis of gut microbiota has been suggested to be associated with the swamp eel’s disease pathogenesis and food digestion. Although the contributions of gut microbiome in fish growth and health has been increasingly recognized, little is known about the microbial community in the intestine of the swamp eel (Monopterus albus). Methods The intestinal microbiomes of the five distinct gut sections (midgut content and mucosa, hindgut content and mucosa, and stools) of swamp eel were compared using Illumina MiSeq sequencing of the bacterial 16S rRNA gene sequence and statistical analysis. Results The results showed that the number of observed OTUs in the intestine decreased proximally to distally. Principal coordinate analysis revealed significant separations among samples from different gut sections. There were 54 core OTUs shared by all gut sections and 36 of these core OTUs varied significantly in their abundances. Additionally, we discovered 66 section-specific enriched KEGG pathways. These section-specific enriched microbial taxa (e.g., Bacillus, Lactobacillus) and potential function capacities (e.g., amino acid metabolism, carbohydrate metabolism) might play vital roles in nutrient metabolism, immune modulation and host-microbe interactions of the swamp eel. Conclusions Our results showed that microbial diversity, composition and function capacity varied substantially across different gut sections. The gut section-specific enriched core microbial taxa and function capacities may perform important roles in swamp eel’s nutrient metabolism, immune modulation, and host-microbe interactions. This study should provide insights into the gut microbiome of the swamp eel.
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Affiliation(s)
- Xuan Chen
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Shaoming Fang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lili Wei
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Qiwang Zhong
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China
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14
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Mullis MM, Rambo IM, Baker BJ, Reese BK. Diversity, Ecology, and Prevalence of Antimicrobials in Nature. Front Microbiol 2019; 10:2518. [PMID: 31803148 PMCID: PMC6869823 DOI: 10.3389/fmicb.2019.02518] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/18/2019] [Indexed: 12/15/2022] Open
Abstract
Microorganisms possess a variety of survival mechanisms, including the production of antimicrobials that function to kill and/or inhibit the growth of competing microorganisms. Studies of antimicrobial production have largely been driven by the medical community in response to the rise in antibiotic-resistant microorganisms and have involved isolated pure cultures under artificial laboratory conditions neglecting the important ecological roles of these compounds. The search for new natural products has extended to biofilms, soil, oceans, coral reefs, and shallow coastal sediments; however, the marine deep subsurface biosphere may be an untapped repository for novel antimicrobial discovery. Uniquely, prokaryotic survival in energy-limited extreme environments force microbial populations to either adapt their metabolism to outcompete or produce novel antimicrobials that inhibit competition. For example, subsurface sediments could yield novel antimicrobial genes, while at the same time answering important ecological questions about the microbial community.
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Affiliation(s)
- Megan M. Mullis
- Department of Life Sciences, Texas A&M University Corpus Christi, Corpus Christi, TX, United States
| | - Ian M. Rambo
- Department of Marine Science, University of Texas Marine Science Institute, Port Aransas, TX, United States
| | - Brett J. Baker
- Department of Marine Science, University of Texas Marine Science Institute, Port Aransas, TX, United States
| | - Brandi Kiel Reese
- Department of Life Sciences, Texas A&M University Corpus Christi, Corpus Christi, TX, United States
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15
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Almeida E, Dias TV, Ferraz G, Carvalho MF, Lage OM. Culturable bacteria from two Portuguese salterns: diversity and bioactive potential. Antonie van Leeuwenhoek 2019; 113:459-475. [PMID: 31720916 DOI: 10.1007/s10482-019-01356-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/28/2019] [Indexed: 11/29/2022]
Abstract
Salterns are extreme environments, where the high salt concentration is the main limitation to microbial growth, along with solar radiation, temperature and pH. These selective pressures might lead to the acquisition of unique genetic adaptations that can manifest in the production of interesting natural products. The present study aimed at obtaining the culturable microbial diversity from two Portuguese salterns located in different geographic regions. A total of 190 isolates were retrieved and identified as belonging to 30 genera distributed among 4 phyla-Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. Specifically, members of the genus Bacillus were the most frequently isolated from both salterns and all actinobacterial isolates belong to the rare members of this group. The molecular screening of NRPS and PKS-I genes allowed the detection of 38 isolates presenting PKS-I, 25 isolates presenting NRPS and 23 isolates presenting both types of biosynthetic genes. Sequencing of randomly selected amplicons revealed similarity with known PKS-I and NRPS genes or non-annotated hypothetical proteins. This study is the first contribution on the culturable bacterial diversity of Portuguese salterns and on their bioactive potential. Ultimately, these findings provide a novel contribution to improve the understanding on the microbial diversity of salterns.
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Affiliation(s)
- Eduarda Almeida
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal. .,Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Porto, Portugal.
| | - Teresa Vale Dias
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Gonçalo Ferraz
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Maria F Carvalho
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Porto, Portugal
| | - Olga M Lage
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Porto, Portugal
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16
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Draft Genome Sequence of Freshwater-Derived Streptomyces sp. Strain BPSDS2, Isolated from Damte Stream, Northeast India. Microbiol Resour Announc 2019; 8:8/43/e00874-19. [PMID: 31649095 PMCID: PMC6813384 DOI: 10.1128/mra.00874-19] [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
We report the draft genome sequence of Streptomyces sp. strain BPSDS2, isolated from freshwater sediments in Northeast India. The draft genome has a size of 8.27 Mb and 7,559 protein-coding sequences.
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17
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Reda RM, Selim KM, El-Sayed HM, El-Hady MA. In Vitro Selection and Identification of Potential Probiotics Isolated from the Gastrointestinal Tract of Nile Tilapia, Oreochromis niloticus. Probiotics Antimicrob Proteins 2019; 10:692-703. [PMID: 28819794 DOI: 10.1007/s12602-017-9314-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fish gut bacteria can be used as probiotics for aquaculture. The aim of this study is to screen and identify beneficial probiotic bacteria from the gut of Nile tilapia, Oreochromis niloticus. Nine out of one hundred thirty-five isolates were non-pathogenic through intraperitoneal injection and had antibacterial activities with at least a strain from the five isolated fish pathogens, Aeromonas sobria, Aeromonas hydrophila, Pseudomonas aeruginosa, Pseudomonas putida, and Staphylococcus aureus. Further tests showed that such isolates can survive in the presence of high bile concentration (10%) and at different acidic pH values. A strains (14HT) was sensitive to all selected antibiotics, two strains were (9HT and 11HT) resistant to streptomycin and three strains (9HT, 11HT and 38HT) had resistance to two antibiotics. Four isolates (11HT, 33HT, 38HT and 41HT) had an amylase and a protease activities and one strain (47HT) showed only amylase activity. Based on 16S rRNA gene analysis, the isolated strains were identified as follows: Lactococcus lactis (8HT, 9HT, 11HT and 33HT); Enterococcus faecalis (14HT), Lysinibacillus sp. (38HT) and Citrobacter freundii (39HT, 41HT and 47HT).
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Affiliation(s)
- Rasha M Reda
- Department of Fish Diseases and Management, Faculty of Veterinary Medicine, Zagazig University, Sharqia, Zagazig, 44511, Egypt
| | - Khaled M Selim
- Department of Fish Diseases and Management, Faculty of Veterinary Medicine, Zagazig University, Sharqia, Zagazig, 44511, Egypt.
| | - Hassanin M El-Sayed
- Department of Fish Diseases and Management, Faculty of Veterinary Medicine, Zagazig University, Sharqia, Zagazig, 44511, Egypt
| | - M A El-Hady
- Department of Fish Diseases and Management, Faculty of Veterinary Medicine, Zagazig University, Sharqia, Zagazig, 44511, Egypt
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18
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Zote J, Passari AK, Zothanpuia, Siddaiah CN, Kumar NS, Abd Allah EF, Hashem A, Alqarawi AA, Malik JA, Singh BP. Phylogenetic affiliation and determination of bioactive compounds of bacterial population associated with organs of mud crab, Scylla olivacea. Saudi J Biol Sci 2018; 25:1743-1754. [PMID: 30591795 PMCID: PMC6303169 DOI: 10.1016/j.sjbs.2018.08.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/25/2018] [Accepted: 08/25/2018] [Indexed: 11/29/2022] Open
Abstract
Mud crab belongs to the genus Scylla is an economically valuable and preferred species for costal aquaculture in Asian countries, including India. In recent years, there has been a tremendous expansion of Scylla farming, which has led to increasing research on its habit and habitats. However, there has been no study undertaken to understand the role of the bacterial population associated with the different organs of the mud crab, Scylla olivacea. In total, 43 isolates were recovered from four selected parts of the crab (carapace, n = 18; abdomen n = 11; leg, n = 8; and hand, n = 6), and the 16S rRNA gene was used to identify the bacterial isolates. The antimicrobial potential along with the detection of modular polyketide synthase (PKSI), cytochrome P450 hydroxylase (CYP) and non-ribosomal peptide synthetase (NRPS) gene clusters were investigated to show a relationship among the biosynthetic genes with their useful aspects. Additionally, the potential three strains (BPS_CRB12, BPS_CRB14 and BPS_CRB41), which showed significant antimicrobial activities, also showed the presence of twenty volatile compounds (VOCs) using GC-MS analysis. We conclude that the strain Aneurinibacillus aneurinilyticus BPS_CRB41 could be source for the production of bioactive compounds.
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Affiliation(s)
- Joanne Zote
- Department of Biotechnology, Aizawl, Mizoram University, Mizoram 796004, India
| | - Ajit Kumar Passari
- Department of Biotechnology, Aizawl, Mizoram University, Mizoram 796004, India
| | - Zothanpuia
- Department of Biotechnology, Aizawl, Mizoram University, Mizoram 796004, India
| | | | | | - Elsayed Fathi Abd Allah
- Plant Production Department, College of Food and Agriculture Science, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Abeer Hashem
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, Riyadh 11451, Saudi Arabia
| | - Abdulaziz A Alqarawi
- Plant Production Department, College of Food and Agriculture Science, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Jahangir Ahmad Malik
- Plant Production Department, College of Food and Agriculture Science, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Bhim Pratap Singh
- Department of Biotechnology, Aizawl, Mizoram University, Mizoram 796004, India
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19
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Zothanpuia, Passari AK, Leo VV, Chandra P, Kumar B, Nayak C, Hashem A, Abd Allah EF, Alqarawi AA, Singh BP. Bioprospection of actinobacteria derived from freshwater sediments for their potential to produce antimicrobial compounds. Microb Cell Fact 2018; 17:68. [PMID: 29729667 PMCID: PMC5935920 DOI: 10.1186/s12934-018-0912-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 04/24/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Actinobacteria from freshwater habitats have been explored less than from other habitats in the search for compounds of pharmaceutical value. This study highlighted the abundance of actinobacteria from freshwater sediments of two rivers and one lake, and the isolates were studied for their ability to produce antimicrobial bioactive compounds. RESULTS 16S rRNA gene sequencing led to the identification of 84 actinobacterial isolates separated into a common genus (Streptomyces) and eight rare genera (Nocardiopsis, Saccharopolyspora, Rhodococcus, Prauserella, Amycolatopsis, Promicromonospora, Kocuria and Micrococcus). All strains that showed significant inhibition potentials were found against Gram-positive, Gram-negative and yeast pathogens. Further, three biosynthetic genes, polyketide synthases type II (PKS II), nonribosomal peptide synthetases (NRPS) and aminodeoxyisochorismate synthase (phzE), were detected in 38, 71 and 29% of the strains, respectively. Six isolates based on their antimicrobial potentials were selected for the detection and quantification of standard antibiotics using ultra performance liquid chromatography (UPLC-ESI-MS/MS) and volatile organic compounds (VOCs) using gas chromatography mass spectrometry (GC/MS). Four antibiotics (fluconazole, trimethoprim, ketoconazole and rifampicin) and 35 VOCs were quantified and determined from the methanolic crude extract of six selected Streptomyces strains. CONCLUSION Infectious diseases still remain one of the leading causes of death globally and bacterial infections caused millions of deaths annually. Culturable actinobacteria associated with freshwater lake and river sediments has the prospects for the production of bioactive secondary metabolites.
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Affiliation(s)
- Zothanpuia
- Molecular Microbiology and Systematics Laboratory, Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Ajit Kumar Passari
- Molecular Microbiology and Systematics Laboratory, Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Vincent Vineeth Leo
- Molecular Microbiology and Systematics Laboratory, Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Preeti Chandra
- SAIF, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow, 226012, India
| | - Brijesh Kumar
- SAIF, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow, 226012, India
| | | | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box. 2460, Riyadh, 11451, Saudi Arabia
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, ARC, Giza, 12511, Egypt
| | - Elsayed Fathi Abd Allah
- Department of Plant Production, Faculty of Food & Agricultural Sciences, P.O. Box. 2460, Riyadh, 11451, Saudi Arabia
| | - Abdulaziz A Alqarawi
- Department of Plant Production, Faculty of Food & Agricultural Sciences, P.O. Box. 2460, Riyadh, 11451, Saudi Arabia
| | - Bhim Pratap Singh
- Molecular Microbiology and Systematics Laboratory, Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India.
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20
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Cuadrat RRC, Ionescu D, Dávila AMR, Grossart HP. Recovering Genomics Clusters of Secondary Metabolites from Lakes Using Genome-Resolved Metagenomics. Front Microbiol 2018. [PMID: 29515540 PMCID: PMC5826242 DOI: 10.3389/fmicb.2018.00251] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. A total of 18 NRPS, 19 PKS, and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Our approach revealed a high potential to recover and study secondary metabolites genes from any aquatic ecosystem.
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Affiliation(s)
- Rafael R C Cuadrat
- Bioinformatics Core Facility, Max Plank Institute for Biology of Ageing, Köln, Germany.,Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | - Danny Ionescu
- Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Alberto M R Dávila
- Computational and Systems Biology Laboratory, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Hans-Peter Grossart
- Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany.,Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany
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21
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KleinJan H, Jeanthon C, Boyen C, Dittami SM. Exploring the Cultivable Ectocarpus Microbiome. Front Microbiol 2017; 8:2456. [PMID: 29312170 PMCID: PMC5732352 DOI: 10.3389/fmicb.2017.02456] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/27/2017] [Indexed: 01/08/2023] Open
Abstract
Coastal areas form the major habitat of brown macroalgae, photosynthetic multicellular eukaryotes that have great ecological value and industrial potential. Macroalgal growth, development, and physiology are influenced by the microbial community they accommodate. Studying the algal microbiome should thus increase our fundamental understanding of algal biology and may help to improve culturing efforts. Currently, a freshwater strain of the brown macroalga Ectocarpus subulatus is being developed as a model organism for brown macroalgal physiology and algal microbiome studies. It can grow in high and low salinities depending on which microbes it hosts. However, the molecular mechanisms involved in this process are still unclear. Cultivation of Ectocarpus-associated bacteria is the first step toward the development of a model system for in vitro functional studies of brown macroalgal–bacterial interactions during abiotic stress. The main aim of the present study is thus to provide an extensive collection of cultivable E. subulatus-associated bacteria. To meet the variety of metabolic demands of Ectocarpus-associated bacteria, several isolation techniques were applied, i.e., direct plating and dilution-to-extinction cultivation techniques, each with chemically defined and undefined bacterial growth media. Algal tissue and algal growth media were directly used as inoculum, or they were pretreated with antibiotics, by filtration, or by digestion of algal cell walls. In total, 388 isolates were identified falling into 33 genera (46 distinct strains), of which Halomonas (Gammaproteobacteria), Bosea (Alphaproteobacteria), and Limnobacter (Betaproteobacteria) were the most abundant. Comparisons with 16S rRNA gene metabarcoding data showed that culturability in this study was remarkably high (∼50%), although several cultivable strains were not detected or only present in extremely low abundance in the libraries. These undetected bacteria could be considered as part of the rare biosphere and they may form the basis for the temporal changes in the Ectocarpus microbiome.
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Affiliation(s)
- Hetty KleinJan
- Sorbonne Universités, CNRS-UPMC, Station Biologique de Roscoff, UMR8227, Integrative Biology of Marine Models, Roscoff, France
| | - Christian Jeanthon
- CNRS, Station Biologique de Roscoff, UMR7144, Adaptation et Diversité en Milieu Marin, Roscoff, France.,Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, UMR7144, Adaptation et Diversité en Milieu Marin, Roscoff, France
| | - Catherine Boyen
- Sorbonne Universités, CNRS-UPMC, Station Biologique de Roscoff, UMR8227, Integrative Biology of Marine Models, Roscoff, France
| | - Simon M Dittami
- Sorbonne Universités, CNRS-UPMC, Station Biologique de Roscoff, UMR8227, Integrative Biology of Marine Models, Roscoff, France
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Zothanpuia, Passari AK, Chandra P, Leo VV, Mishra VK, Kumar B, Singh BP. Production of Potent Antimicrobial Compounds from Streptomyces cyaneofuscatus Associated with Fresh Water Sediment. Front Microbiol 2017; 8:68. [PMID: 28179900 PMCID: PMC5263160 DOI: 10.3389/fmicb.2017.00068] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/11/2017] [Indexed: 11/27/2022] Open
Abstract
The genus Streptomyces under phylum actinobacteria has been recognized as a prolific source for the production of bioactive secondary metabolites. An actinobacterial strain designated as DST103 isolated from a wetland fresh water sediment of Tamdil Lake, Mizoram, Northeast, India was identified as Streptomyces cyaneofuscatus (KY287599) using 16SrRNA gene sequencing which shares 99.87% sequence similarity with Streptomyces cyaneofuscatus NRRL B-2570T. The strain showed broad spectrum antimicrobial activities against Gram negative bacteria (Escherichia coli MTCC 739 and Pseudomonas aeruginosa MTCC 2453), Gram positive bacteria (Micrococcus luteus NCIM 2170 and Staphylococcus aureus MTCC 96) and yeast pathogen Candida albicans MTCC 3017). The methanolic extract of the strain DST103 exhibited highest antimicrobial activity against E. coli (IC50 = 2.10 μg/mL) and minimum activity against S. aureus (IC50 = 43.63 μg/mL). Five antibiotics [trimethoprim (18 μg/g), fluconazole (6 μg/g), ketoconazole (18 μg/g), nalidixic acid (135 μg/g), and rifampicin (56 μg/g)] were detected and quantified using ultra-performance liquid chromatography (UPLC-ESI-MS/MS). Further, biosynthetic potential genes [polyketide synthases type II, non-ribosomal peptide synthetases, and aminodeoxyisochorismate synthase (phzE)] were also detected in strain DST103 which may possibly be responsible for the production of antimicrobial compounds. Additionally, gas chromatography-mass spectrometry analysis showed the presence of four volatile compounds which might be responsible for their diverse biological activity. The present study revealed the presence of bioactive compounds in strain DST103, which may be a promising resource for the discovery of novel bioactive metabolites against wide range of pathogens.
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Affiliation(s)
- Zothanpuia
- Molecular Microbiology and Systematics Laboratory, Department of Biotechnology, Mizoram University Aizawl, India
| | - Ajit K Passari
- Molecular Microbiology and Systematics Laboratory, Department of Biotechnology, Mizoram University Aizawl, India
| | - Preeti Chandra
- CSIR-Central Drug Research Institute, Sophisticated Analytical Instrument Facility Lucknow, India
| | - Vincent V Leo
- Molecular Microbiology and Systematics Laboratory, Department of Biotechnology, Mizoram University Aizawl, India
| | - Vineet K Mishra
- Molecular Microbiology and Systematics Laboratory, Department of Biotechnology, Mizoram University Aizawl, India
| | - Brijesh Kumar
- CSIR-Central Drug Research Institute, Sophisticated Analytical Instrument Facility Lucknow, India
| | - Bhim P Singh
- Molecular Microbiology and Systematics Laboratory, Department of Biotechnology, Mizoram University Aizawl, India
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