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Baranova MN, Pilipenko EA, Gabibov AG, Terekhov SS, Smirnov IV. Animal Microbiomes as a Source of Novel Antibiotic-Producing Strains. Int J Mol Sci 2023; 25:537. [PMID: 38203702 PMCID: PMC10779147 DOI: 10.3390/ijms25010537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Natural compounds continue to serve as the most fruitful source of new antimicrobials. Analysis of bacterial genomes have revealed that the biosynthetic potential of antibiotic producers by far exceeds the number of already discovered structures. However, due to the repeated discovery of known substances, it has become necessary to change both approaches to the search for antibiotics and the sources of producer strains. The pressure of natural selection and the diversity of interactions in symbiotic communities make animal microbiomes promising sources of novel substances. Here, microorganisms associated with various animals were examined in terms of their antimicrobial agents. The application of alternative cultivation techniques, ultrahigh-throughput screening, and genomic analysis facilitated the investigation of compounds produced by unique representatives of the animal microbiota. We believe that new strategies of antipathogen defense will be discovered by precisely studying cell-cell and host-microbe interactions in microbiomes in the wild.
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Affiliation(s)
- Margarita N. Baranova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
| | - Ekaterina A. Pilipenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
| | - Alexander G. Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Stanislav S. Terekhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan V. Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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Rathinam AJ, Santhaseelan H, Dahms HU, Dinakaran VT, Murugaiah SG. Bioprospecting of unexplored halophilic actinobacteria against human infectious pathogens. 3 Biotech 2023; 13:398. [PMID: 37974926 PMCID: PMC10645811 DOI: 10.1007/s13205-023-03812-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 10/08/2023] [Indexed: 11/19/2023] Open
Abstract
Human pathogenic diseases received much attention recently due to their uncontrolled spread of antimicrobial resistance (AMR) which causes several threads every year. Effective alternate antimicrobials are urgently required to combat those disease causing infectious microbes. Halophilic actinobacteria revealed huge potentials and unexplored cultivable/non-cultivable actinobacterial species producing enormous antimicrobials have been proved in several genomics approaches. Potential gene clusters, PKS and NRPKS from Nocardia, Salinospora, Rhodococcus, and Streptomyces have wide range coding genes of secondary metabolites. Biosynthetic pathways identification via various approaches like genome mining, In silico, OSMAC (one strain many compound) analysis provides better identification of knowing the active metabolites using several databases like AMP, APD and CRAMPR, etc. Genome constellations of actinobacteria particularly the prediction of BGCs (Biosynthetic Gene Clusters) to mine the bioactive molecules such as pigments, biosurfactants and few enzymes have been reported for antimicrobial activity. Saltpan, saltlake, lagoon and haloalkali environment exploring potential actinobacterial strains Micromonospora, Kocuria, Pseudonocardia, and Nocardiopsis revealed several acids and ester derivatives with antimicrobial potential. Marine sediments and marine macro organisms have been found as significant population holders of potential actinobacterial strains. Deadly infectious diseases (IDs) including tuberculosis, ventilator-associated pneumonia and Candidiasis, have been targeted by halo-actinobacterial metabolites with promising results. Methicillin resistant Staphylococus aureus and virus like Encephalitic alphaviruses were potentially targeted by halophilic actinobacterial metabolites by the compound Homoseongomycin from sponge associated antinobacterium. In this review, we discuss the potential antimicrobial properties of various biomolecules extracted from the unexplored halophilic actinobacterial strains specifically against human infectious pathogens along with prospective genomic constellations.
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Affiliation(s)
- Arthur James Rathinam
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620 024 India
| | - Henciya Santhaseelan
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620 024 India
| | - Hans-Uwe Dahms
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, 80708 Taiwan
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Kakakhel MA, Narwal N, Kataria N, Johari SA, Zaheer Ud Din S, Jiang Z, Khoo KS, Xiaotao S. Deciphering the dysbiosis caused in the fish microbiota by emerging contaminants and its mitigation strategies-A review. ENVIRONMENTAL RESEARCH 2023; 237:117002. [PMID: 37648194 DOI: 10.1016/j.envres.2023.117002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/01/2023]
Abstract
The primary barrier to nutrient absorption in fish is the intestinal epithelium, followed by a community of microorganisms known as the gut microbiota, which can be thought of as a hidden organ. The gastrointestinal microbiota of fish plays a key role in the upholding of overall health by maintaining the homeostasis and disease resistance of the host. However, emerging contaminants as the result of anthropogenic activities have significantly led to disruptions and intestinal dysbiosis in fish. Which probably results in fish mortalities and disrupts the balance of an ecosystem. Therefore, we comprehensively seek to compile the effects and consequences of emerging contaminations on fish intestinal microbiota. Additionally, the mitigation strategies including prebiotics, probiotics, plant-based diet, and Biofloc technology are being outlined. Biofloc technology (BFT) can treat toxic materials, i.e., nitrogen components, and convert them into a useful product such as proteins and demonstrated promising elevating technique for the fish intestinal bacterial composition. However, it remains unclear whether the bacterial isolate is primarily responsible for the BFT's removal of nitrate and ammonia and the corresponding removal mechanism. To answer this, real time polymerase chain reaction (RT-PCR) with metagenomics, transcriptomics, and proteomics techniques probably provides a possible solution.
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Affiliation(s)
- Mian Adnan Kakakhel
- Hubei International Science and Technology Cooperation Base of Fish Passage, Three Gorges University, Yichang, 443002, Hubei, China; College of Hydraulic & Environmental Engineering, Three Gorges University, Yichang, 443002, Hubei, China
| | - Nishita Narwal
- University School of Environment Management, Guru Gobind Singh Indraprastha University, New Delhi, 110078, India
| | - Navish Kataria
- Department of Environmental Sciences, J.C. Bose University of Science and Technology, YMCA, Faridabad, Haryana, 121006, India
| | - Seyed Ali Johari
- Department of Fisheries, Faculty of Natural Resources, University of Kurdistan, Sanandaj, Kurdistan, Iran
| | - Syed Zaheer Ud Din
- International School for Optoelectronic Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Zewen Jiang
- Hubei International Science and Technology Cooperation Base of Fish Passage, Three Gorges University, Yichang, 443002, Hubei, China; College of Hydraulic & Environmental Engineering, Three Gorges University, Yichang, 443002, Hubei, China
| | - Kuan Shiong Khoo
- Department of Chemical Engineering and Materials Science, Yuan Ze University, Taoyuan, Taiwan
| | - Shi Xiaotao
- Hubei International Science and Technology Cooperation Base of Fish Passage, Three Gorges University, Yichang, 443002, Hubei, China; College of Hydraulic & Environmental Engineering, Three Gorges University, Yichang, 443002, Hubei, China.
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4
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Kochetkov N, Smorodinskaya S, Vatlin A, Nikiforov-Nikishin D, Nikiforov-Nikishin A, Danilenko V, Anastasia K, Reznikova D, Grishina Y, Antipov S, Marsova M. Ability of Lactobacillus brevis 47f to Alleviate the Toxic Effects of Imidacloprid Low Concentration on the Histological Parameters and Cytokine Profile of Zebrafish ( Danio rerio). Int J Mol Sci 2023; 24:12290. [PMID: 37569666 PMCID: PMC10418720 DOI: 10.3390/ijms241512290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 07/27/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
In the present article, the possible mitigation of the toxic effect of imidacloprid low-concentration chronic exposure on Danio rerio by the probiotic strain Lactobacillus brevis 47f (1 × 108 CFU/g) was examined. It was found that even sublethal concentration (2500 µg/L) could lead to the death of some fish during the 60-day chronic experiment. However, the use of Lactobacillus brevis 47f partially reduced the toxic effects, resulting in an increased survival rate and a significant reduction of morphohistological lesions in the intestines and kidneys of Danio rerio. The kidneys were found to be the most susceptible organ to toxic exposure, showing significant disturbances. Calculation of the histopathological index, measurement of morphometric parameters, and analysis of principal components revealed the most significant parameters affected by the combined action of imidacloprid and Lactobacillus brevis 47f. This effect of imidacloprid and the probiotic strain had a multidirectional influence on various pro/anti-inflammatory cytokines (IL-1β, TNF-α, IL-6, IL-8). Therefore, the results suggest the possibility of further studying the probiotic strain Lactobacillus brevis 47f as a strain that reduces the toxic effects of xenobiotics. Additionally, the study established the possibility of using imidacloprid as a model toxicant to assess the detoxification ability of probiotics on the kidney and gastrointestinal tract of fish.
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Affiliation(s)
- Nikita Kochetkov
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (S.S.); (A.V.); (D.N.-N.); (V.D.); (K.A.); (D.R.); (Y.G.)
- Faculty of Biotechnology and Fisheries, Moscow State University of Technologies and Management (FCU), 73, Zemlyanoy Val Str., 109004 Moscow, Russia;
| | - Svetlana Smorodinskaya
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (S.S.); (A.V.); (D.N.-N.); (V.D.); (K.A.); (D.R.); (Y.G.)
- Faculty of Biotechnology and Fisheries, Moscow State University of Technologies and Management (FCU), 73, Zemlyanoy Val Str., 109004 Moscow, Russia;
| | - Aleksey Vatlin
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (S.S.); (A.V.); (D.N.-N.); (V.D.); (K.A.); (D.R.); (Y.G.)
| | - Dmitry Nikiforov-Nikishin
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (S.S.); (A.V.); (D.N.-N.); (V.D.); (K.A.); (D.R.); (Y.G.)
- Faculty of Biotechnology and Fisheries, Moscow State University of Technologies and Management (FCU), 73, Zemlyanoy Val Str., 109004 Moscow, Russia;
| | - Alexei Nikiforov-Nikishin
- Faculty of Biotechnology and Fisheries, Moscow State University of Technologies and Management (FCU), 73, Zemlyanoy Val Str., 109004 Moscow, Russia;
| | - Valery Danilenko
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (S.S.); (A.V.); (D.N.-N.); (V.D.); (K.A.); (D.R.); (Y.G.)
| | - Klimuk Anastasia
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (S.S.); (A.V.); (D.N.-N.); (V.D.); (K.A.); (D.R.); (Y.G.)
- Faculty of Biotechnology and Fisheries, Moscow State University of Technologies and Management (FCU), 73, Zemlyanoy Val Str., 109004 Moscow, Russia;
| | - Diana Reznikova
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (S.S.); (A.V.); (D.N.-N.); (V.D.); (K.A.); (D.R.); (Y.G.)
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Institutsky Lane 9, 141700 Dolgoprudny, Russia
| | - Yelena Grishina
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (S.S.); (A.V.); (D.N.-N.); (V.D.); (K.A.); (D.R.); (Y.G.)
| | - Sergei Antipov
- Department of Biophysics and Biotechnology, Voronezh State University, University Square, 1, 394063 Voronezh, Russia;
| | - Maria Marsova
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (S.S.); (A.V.); (D.N.-N.); (V.D.); (K.A.); (D.R.); (Y.G.)
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Ashwin RK, Aruna A, Koyyodan J, Kaari M, Venugopal G, Manikkam R. Exploration of fish gut-associated actinobacteria for its antifouling activity. J Basic Microbiol 2023. [PMID: 37127854 DOI: 10.1002/jobm.202300051] [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: 02/05/2023] [Revised: 04/03/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
An attempt has been made to screen the fish gut-associated actinobacterial cultures for antifouling compounds. Fifteen morphologically distinct bacterial cultures were recovered from the biofouling samples scraped from the boat surfaces and other maritime structures in the Kovalam beach (Lat. 12.7870°N; Long. 80.2504°E) coastal areas in Tamil Nadu, India. All the bacterial isolates were identified at generic level from which two isolates namely KB6 and KB7 as Staphylococcus sp. were found the exhibit strong biofilm formation. Four actinobacterial strains viz., IM20, PYA9, F8, and SQA4 were evaluated for inhibitory properties against biofouling bacteria using the agar plug method. Strain IM20 which strongly inhibited the biofouling bacteria was chosen as prospective strain for further studies. When compared to submerged fermentation, IM20 produced a high amount of antifouling chemicals on the agar surface fermentation. Among the solvents tested, better extraction of antifouling compounds was seen in ethyl acetate extract. Antifouling compound production by the strain IM20 was found to be influenced by a number of variables such as glucose, fructose, glutamine, malt extract, pH 7 and 9, temperature 30 and 40° C and NaCl at 2.5% and 5% concentrations. Gas chromatography-mass spectrometry (GC-MS) analysis of the strain IM20 extract revealed the presence of pyrrolo (1,2-a]pyrazine-1,4-dione, hexahydro) in significant amount. In the present study, the fish gut-associated Streptomyces sp. IM20 was identified as an unusual and newly added source for the isolation of antifouling compounds.
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Affiliation(s)
- Ramesh K Ashwin
- Department of Biotechnology, Madha Engineering College, Kundrathur, Chennai, India
| | - Arunachalam Aruna
- Department of Biotechnology, Madha Engineering College, Kundrathur, Chennai, India
| | - Jisha Koyyodan
- Department of Microbiology, Vels Institute of Science, Technology and Advanced Studies, Chennai, India
| | - Manigundan Kaari
- Centre for Drug Discovery and Development, Sathyabama Institute for Science and Technology, Chennai, India
| | - Gopikrishnan Venugopal
- Centre for Drug Discovery and Development, Sathyabama Institute for Science and Technology, Chennai, India
| | - Radhakrishnan Manikkam
- Centre for Drug Discovery and Development, Sathyabama Institute for Science and Technology, Chennai, India
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Jang WJ, Lee KB, Jeon MH, Lee SJ, Hur SW, Lee S, Lee BJ, Lee JM, Kim KW, Lee EW. Characteristics and biological control functions of Bacillus sp. PM8313 as a host-associated probiotic in red sea bream ( Pagrus major) aquaculture. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2023; 12:20-31. [PMID: 36381063 PMCID: PMC9641168 DOI: 10.1016/j.aninu.2022.08.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 07/29/2022] [Accepted: 08/10/2022] [Indexed: 06/16/2023]
Abstract
Host-associated probiotics (HAPs) are bacteria originally isolated from rearing water or the host's gastrointestinal tract in order to enhance the host's growth and health. This study investigated the HAP potential of Bacillus sp. PM8313, isolated from wild red sea bream (Pagrus major), through characterization and feeding trials. Results based on in vitro tests showed that PM8313 is safe, confirming its hemolytic, cytotoxic, and antibiotic resistance. In addition, PM8313 showed advantages as a probiotic with high viability in the gastrointestinal model and a high cell adhesion rate. Whole-genome sequencing demonstrated that PM8313 has a 4,615,871 bp single circular chromosome and a guanine-cytosine content of 45.25%. It also showed the absence of genes encoding virulence factors, such as cytotoxin, enterotoxin, hemolysin, sphingomyelinase, and phospholipase. In the feeding trial, a supplemental diet of 1 × 108 CFU/g PM8313 positively altered the weight gain, digestive enzyme activity, and intestinal microbiota composition of red sea bream. Analysis of nonspecific immune parameters and immune-related gene expression, and a challenge test showed that PM8313 supplementation increases immunity and pathogenic bacteria resistance. Our findings suggest that PM8313 should be considered for application as a novel HAP to red sea bream aquaculture.
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Affiliation(s)
- Won Je Jang
- Department of Biotechnology, Pukyong National University, Busan, 48513, South Korea
| | - Kyung-Bon Lee
- Department of Biology Education College of Education, Chonnam National University, Gwangju, 61186, South Korea
| | - Mi-Hyeon Jeon
- Biopharmaceutical Engineering Major, Division of Applied Bioengineering, Dong-Eui University, Busan, 47340, South Korea
| | - Su-Jeong Lee
- Biopharmaceutical Engineering Major, Division of Applied Bioengineering, Dong-Eui University, Busan, 47340, South Korea
| | - Sang Woo Hur
- Aquafeed Research Center, National Institute of Fisheries Science, Pohang, 37517, South Korea
| | - Seunghan Lee
- Aquafeed Research Center, National Institute of Fisheries Science, Pohang, 37517, South Korea
| | - Bong-Joo Lee
- Aquafeed Research Center, National Institute of Fisheries Science, Pohang, 37517, South Korea
- Department of Smart Fisheries Resources, College of Industrial Sciences, Kongju National University, Yesan, 32439, South Korea
| | - Jong Min Lee
- Department of Biotechnology, Pukyong National University, Busan, 48513, South Korea
| | - Kang-Woong Kim
- Aquafeed Research Center, National Institute of Fisheries Science, Pohang, 37517, South Korea
| | - Eun-Woo Lee
- Biopharmaceutical Engineering Major, Division of Applied Bioengineering, Dong-Eui University, Busan, 47340, South Korea
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Ghotbi M, Kelting O, Blümel M, Tasdemir D. Gut and Gill-Associated Microbiota of the Flatfish European Plaice ( Pleuronectes platessa): Diversity, Metabolome and Bioactivity against Human and Aquaculture Pathogens. Mar Drugs 2022; 20:md20090573. [PMID: 36135762 PMCID: PMC9500656 DOI: 10.3390/md20090573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/29/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Similar to other marine holobionts, fish are colonized by complex microbial communities that promote their health and growth. Fish-associated microbiota is emerging as a promising source of bioactive metabolites. Pleuronectes platessa (European plaice, plaice), a flatfish with commercial importance, is common in the Baltic Sea. Here we used a culture-dependent survey followed by molecular identification to identify microbiota associated with the gills and the gastrointestinal tract (GIT) of P. platessa, then profiled their antimicrobial activity and metabolome. Altogether, 66 strains (59 bacteria and 7 fungi) were isolated, with Proteobacteria being the most abundant phylum. Gill-associated microbiota accounted for higher number of isolates and was dominated by the Proteobacteria (family Moraxellaceae) and Actinobacteria (family Nocardiaceae), whereas Gram-negative bacterial families Vibrionaceae and Shewanellaceae represented the largest group associated with the GIT. The EtOAc extracts of the solid and liquid media cultures of 21 bacteria and 2 fungi representing the diversity of cultivable plaice-associated microbiota was profiled for their antimicrobial activity against three fish pathogens, human bacterial pathogen panel (ESKAPE) and two human fungal pathogens. More than half of all tested microorganisms, particularly those originating from the GIT epithelium, exhibited antagonistic effect against fish pathogens (Lactococcus garvieae, Vibrio ichthyoenteri) and/or human pathogens (Enterococcus faecium, methicillin-resistant Staphylococcus aureus). Proteobacteria represented the most active isolates. Notably, the solid media extracts displayed higher activity against fish pathogens, while liquid culture extracts were more active against human pathogens. Untargeted metabolomics approach using feature-based molecular networking showed the high chemical diversity of the liquid extracts that contained undescribed clusters. This study highlights plaice-associated microbiota as a potential source of antimicrobials for the control of human and the aquaculture-associated infections. This is the first study reporting diversity, bioactivity and chemical profile of culture-dependent microbiota of plaice.
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Affiliation(s)
- Marjan Ghotbi
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
| | - Ole Kelting
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
- Faculty of Mathematics and Natural Sciences, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
- Correspondence: ; Tel.: +49-431-600-4430
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Villegas-Plazas M, Villamil L, Martínez-Silva MA, González-Jiménez T, Salazar M, Güiza L, Mendoza M, Junca H. Microbiome composition and autochthonous probiotics from contrasting probiosis/dysbiosis states in cobia (Rachycentron canadum) fish epitheliocystis. Access Microbiol 2022; 4:acmi000405. [PMID: 36133177 PMCID: PMC9484664 DOI: 10.1099/acmi.0.000405] [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: 01/12/2022] [Accepted: 06/24/2022] [Indexed: 11/18/2022] Open
Abstract
Microbiome components and bacterial isolates related to healthy and epitheliocystis states in aquaculture cycles of cobia fish were studied. We detected well-defined 16S rRNA amplicon gene sequence variants showing differential abundance in healthy or diseased cycles. Isolation trials were performed, and experimental tests were used to determine probiotic potential of the bacterial strains obtained from water, tissues or live food used in this aquaculture model. The taxonomic affiliation of these strains was cross-compared against microbiome components, finding that some of them had close or identical affiliation to the abundant types found in healthy cycles. Strains belonging to the groups already identified as predominant by culture-independent means were screened as potential probiotics based on desirable activities such as antagonism and antibiosis against marine pathogenic bacteria, quorum quenching, bile acid resistance, antibiotic sensitivity and enzymatic activities for improved nutrient digestion. We have also found that in the tracking of microbiome composition across different developmental stages of cobia, healthy cycles exhibited a consistent high relative abundance of a Mesobacillus sp., while in the diseased cycle the emergence of a Vibrio sp. was observed. Our study suggests that epithelocystis in cobia is associated with a displacement of a symbiotic microbiome community linked to the increase frequency of Vibrio species.
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Affiliation(s)
- Marcela Villegas-Plazas
- RG Microbial Ecology: Metabolism, Genomics & Evolutions, Div. Ecogenomics & Holobionts, Microbiomas Foundation, Chia, Colombia
| | - Luisa Villamil
- Programa de Doctorado en Biociencias, Facultad de Ingeniería, Universidad de la Sabana, Chía, Colombia
- Universidad Jorge Tadeo Lozano, Sede Santa Marta, Colombia
| | - María Angélica Martínez-Silva
- Université du Québec à Rimouski, Institute des Sciences de la Mer à Rimouski, Québec, Canada
- Universidad Jorge Tadeo Lozano, Sede Santa Marta, Colombia
| | | | - Marcela Salazar
- Benchmark Genetics Colombia, Punta Canoas, Cartagena, Colombia
- Corporación CorpoGen, Bogotá, Colombia
| | - Linda Güiza
- Benchmark Genetics Colombia, Punta Canoas, Cartagena, Colombia
| | - Mabel Mendoza
- Centro de Investigación de la Acuicultura en Colombia, Ceniacua, Cartagena, Colombia
| | - Howard Junca
- RG Microbial Ecology: Metabolism, Genomics & Evolutions, Div. Ecogenomics & Holobionts, Microbiomas Foundation, Chia, Colombia
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Jang WJ, Jeon MH, Lee SJ, Park SY, Lee YS, Noh DI, Hur SW, Lee S, Lee BJ, Lee JM, Kim KW, Lee EW, Hasan MT. Dietary Supplementation of Bacillus sp. PM8313 with β-glucan Modulates the Intestinal Microbiota of Red Sea Bream ( Pagrus major) to Increase Growth, Immunity, and Disease Resistance. Front Immunol 2022; 13:960554. [PMID: 35935938 PMCID: PMC9353131 DOI: 10.3389/fimmu.2022.960554] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
A 56-day feeding trial was conducted to determine the effect of dietary supplementation with Bacillus sp. isolated from the intestines of red sea bream on the growth performance, immunity, and gut microbiome composition of red sea bream. Three diets (a control diet and two treatments) were formulated without Bacillus sp. PM8313 or β-glucan (control, CD), 1 × 108 CFU g-1 PM8313 (BSD), and 1 × 108 CFU g-1 PM8313 + 0.1% β-glucan (BGSD). At the end of the experiment, the weight, specific growth rate, feed conversion ratio, and protein efficiency ratio of the fish in the BSD and BGSD diet groups were significantly improved than those of the control group (P < 0.05). Additionally, amylase and trypsin activities were significantly higher (P < 0.05) in both groups compared to the control. Superoxide dismutase and lysozyme activity, which are serum non-specific immune responses, only increased in the BGSD group. The two treatment groups exhibited a marked difference in the intestinal microbiota composition compared to the control group. Furthermore, the treatment groups exhibited an upregulation of IL-6 and NF-κb, coupled with high survival rates when challenged with Edwardsiella tarda. Therefore, dietary supplementation with PM8313 improved the growth performance, digestive enzyme activity, non-specific immunity, and pathogen resistance of red sea bream, in addition to affecting the composition of its intestinal microflora.
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Affiliation(s)
- Won Je Jang
- Department of Biotechnology, Pukyong National University, Busan, South Korea
| | - Mi-Hyeon Jeon
- Biopharmaceutical Engineering Major, Division of Applied Bioengineering, Dong-Eui University, Busan, South Korea
| | - Su-Jeong Lee
- Biopharmaceutical Engineering Major, Division of Applied Bioengineering, Dong-Eui University, Busan, South Korea
| | - So Young Park
- Department of Biotechnology, Pukyong National University, Busan, South Korea
| | - Young-Sun Lee
- Biopharmaceutical Engineering Major, Division of Applied Bioengineering, Dong-Eui University, Busan, South Korea
| | - Da-In Noh
- Biopharmaceutical Engineering Major, Division of Applied Bioengineering, Dong-Eui University, Busan, South Korea
| | - Sang Woo Hur
- Aquafeed Research Center, National Institute of Fisheries Science, Pohang, South Korea
| | - Seunghan Lee
- Aquafeed Research Center, National Institute of Fisheries Science, Pohang, South Korea
| | - Bong-Joo Lee
- Aquafeed Research Center, National Institute of Fisheries Science, Pohang, South Korea
- Department of Smart Fisheries Resources, College of Industrial Sciences, Kongju National University, Yesan, South Korea
| | - Jong Min Lee
- Department of Biotechnology, Pukyong National University, Busan, South Korea
| | - Kang-Woong Kim
- Aquafeed Research Center, National Institute of Fisheries Science, Pohang, South Korea
| | - Eun-Woo Lee
- Biopharmaceutical Engineering Major, Division of Applied Bioengineering, Dong-Eui University, Busan, South Korea
- Core-Facility Center for Tissue Regeneration, Dong-Eui University, Busan, South Korea
| | - Md Tawheed Hasan
- Core-Facility Center for Tissue Regeneration, Dong-Eui University, Busan, South Korea
- Department of Aquaculture, Sylhet Agricultural University, Sylhet, Bangladesh
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10
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Wang J, Wu Z, Wang S, Wang X, Zhang D, Wang Q, Lin L, Wang G, Guo Z, Chen Y. Inhibitory effect of probiotic Bacillus spp. isolated from the digestive tract of Rhynchocypris Lagowskii on the adhesion of common pathogenic bacteria in the intestinal model. Microb Pathog 2022; 169:105623. [PMID: 35691482 DOI: 10.1016/j.micpath.2022.105623] [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: 03/01/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022]
Abstract
Diseases of fish caused by pathogenic bacteria are an important constraint on aquaculture production. Antibiotics have been widely used to control infectious diseases, but this has led to the emergence of drug-resistant bacteria and affected human health. In this context, probiotics are used as an alternative to antibiotics for the prevention and control of diseases in aquaculture. The aim of this study was to obtain probiotic candidate strains of Bacillus spp. from the gut of Rhynchocypris Lagowskii. Strains were screened by enzyme-producing ability, antagonism assay and antibiotic susceptibility. The safety of the strains to host fish has also been established. The isolated Bacillus licheniformis (LSG1-1) and Bacillus subtilis (LSG2-1) were characterized and performed well in tolerance experiments. In addition, LSG1-1 and LSG2-1 were detected to have higher self-aggregation ability and surface hydrophobicity. In the in vitro adhesion model, LSG1-1 and LSG2-1 showed good adhesion ability and had obvious adhesion inhibitory effect on three pathogens of Aeromonas. Based on the characteristics observed so far, Bacillus licheniformis LSG1-1 and Bacillus subtilis LSG2-1 could form potential probiotic candidates in the digestive tract of R. lagowskii to help combat diseases in aquaculture.
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Affiliation(s)
- Jiajing Wang
- College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Nutrition and Feed Science, Jilin Agricultural University, Changchun, 130118, China
| | - Zhenchao Wu
- College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Nutrition and Feed Science, Jilin Agricultural University, Changchun, 130118, China
| | - Seng Wang
- College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Nutrition and Feed Science, Jilin Agricultural University, Changchun, 130118, China
| | - Xin Wang
- College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Nutrition and Feed Science, Jilin Agricultural University, Changchun, 130118, China
| | - Dongming Zhang
- College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Nutrition and Feed Science, Jilin Agricultural University, Changchun, 130118, China
| | - Qiuju Wang
- College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Nutrition and Feed Science, Jilin Agricultural University, Changchun, 130118, China
| | - Lili Lin
- Fisheries Technology Promotion Station of Jilin Province, Changchun, 130012, China
| | - Guiqin Wang
- College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Nutrition and Feed Science, Jilin Agricultural University, Changchun, 130118, China
| | - Zhixin Guo
- College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Nutrition and Feed Science, Jilin Agricultural University, Changchun, 130118, China; College of Life Sciences, Tonghua Normal University, Tonghua, 134001, China
| | - Yuke Chen
- College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Nutrition and Feed Science, Jilin Agricultural University, Changchun, 130118, China.
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11
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Extremophilic Fungi from Marine Environments: Underexplored Sources of Antitumor, Anti-Infective and Other Biologically Active Agents. Mar Drugs 2022; 20:md20010062. [PMID: 35049917 PMCID: PMC8781577 DOI: 10.3390/md20010062] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/07/2023] Open
Abstract
Marine environments are underexplored terrains containing fungi that produce a diversity of natural products given unique environmental pressures and nutrients. While bacteria are commonly the most studied microorganism for natural products in the marine world, marine fungi are also abundant but remain an untapped source of bioactive metabolites. Given that their terrestrial counterparts have been a source of many blockbuster antitumor agents and anti-infectives, including camptothecin, the penicillins, and cyclosporin A, marine fungi also have the potential to produce new chemical scaffolds as leads to potential drugs. Fungi are more phylogenetically diverse than bacteria and have larger genomes that contain many silent biosynthetic gene clusters involved in making bioactive compounds. However, less than 5% of all known fungi have been cultivated under standard laboratory conditions. While the number of reported natural products from marine fungi is steadily increasing, their number is still significantly lower compared to those reported from their bacterial counterparts. Herein, we discuss many varied cytotoxic and anti-infective fungal metabolites isolated from extreme marine environments, including symbiotic associations as well as extreme pressures, temperatures, salinity, and light. We also discuss cultivation strategies that can be used to produce new bioactive metabolites or increase their production. This review presents a large number of reported structures though, at times, only a few of a large number of related structures are shown.
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12
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Shrimp production, the most important diseases that threaten it, and the role of probiotics in confronting these diseases: A review. Res Vet Sci 2022; 144:126-140. [DOI: 10.1016/j.rvsc.2022.01.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/21/2021] [Accepted: 01/12/2022] [Indexed: 12/13/2022]
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13
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Partial Purification and Characterization of Bacteriocin-Like Inhibitory Substances Produced by Streptomyces sp. Isolated from the Gut of Chanos chanos. BIOMED RESEARCH INTERNATIONAL 2021; 2021:7190152. [PMID: 34950735 PMCID: PMC8692027 DOI: 10.1155/2021/7190152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/08/2021] [Accepted: 11/30/2021] [Indexed: 11/17/2022]
Abstract
Bacteriocin-like inhibitory substances (BLIS) have sparked great interest because of their promising use in food as natural antimicrobial agents. In this work, six Streptomyces isolates obtained from the gut of Chanos chanos demonstrated their ability to produce extracellular metabolites with inhibitory activity against Salmonella enterica serovar Typhimurium, Escherichia coli, Listeria monocytogenes, and Staphylococcus aureus. Exposure of the extracellular metabolites to proteolytic enzymes (i.e., proteinase-K, trypsin, and pepsin) revealed high sensitivity and confirmed their proteinaceous nature. The metabolites were stable at high temperatures (up to 100°C for 30 min) and a wide range of pH (pH 2.0–7.0). Fractionation of the crude BLIS by filtration yielded three fractions based on molecular weight: <3 kDa, 3–10 kDa, and >10 kDa. Analysis of the antibacterial activity of these fractions showed increased specific activity, especially in the fraction with a molecular weight (MW) of <3 kDa, relative to the crude sample. The fraction with MW < 3 kDa had minimum inhibitory and bactericidal concentrations in ranges 0.04–0.62 mg·mL−1 and 0.08–1.25 mg·mL−1, respectively. This fraction also showed better temperature and pH stability compared with crude BLIS. Brine shrimp toxicity assay revealed that this fraction has moderate toxicity with a 50% lethal concentration of 226.975 μg·mL−1 (i.e., moderate toxicity) to Artemia salina. Identification of the peptide sequences of this fraction by liquid chromatography–tandem mass spectrometry yielded 130 proteins with retention times of 15.21–19.57 min. Eleven proteins with MWs of 1345.66–2908.35 Da and composed of less than 30 amino acid residues with high hydrophobicity (15.34–26.22 kcal·mol−1) appeared to be responsible for the antibacterial activity of the fraction. This study revealed the potential application of BLIS from Streptomyces, especially BLIS SCA-8, as antibacterial agents.
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14
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Diwan AD, Harke SN, Gopalkrishna, Panche AN. Aquaculture industry prospective from gut microbiome of fish and shellfish: An overview. J Anim Physiol Anim Nutr (Berl) 2021; 106:441-469. [PMID: 34355428 DOI: 10.1111/jpn.13619] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/17/2021] [Accepted: 07/20/2021] [Indexed: 12/17/2022]
Abstract
The microbiome actually deals with micro-organisms that are associated with indigenous body parts and the entire gut system in all animals, including human beings. These microbes are linked with roles involving hereditary traits, defence against diseases and strengthening overall immunity, which determines the health status of an organism. Considerable efforts have been made to find out the microbiome diversity and their taxonomic identification in finfish and shellfish and its importance has been correlated with various physiological functions and activities. In recent past due to the availability of advanced molecular tools, some efforts have also been made on DNA sequencing of these microbes to understand the environmental impact and other stress factors on their genomic structural profile. There are reports on the use of next-generation sequencing (NGS) technology, including amplicon and shot-gun approaches, and associated bioinformatics tools to count and classify commensal microbiome at the species level. The microbiome present in the whole body, particularly in the gut systems of finfish and shellfish, not only contributes to digestion but also has an impact on nutrition, growth, reproduction, immune system and vulnerability of the host fish to diseases. Therefore, the study of such microbial communities is highly relevant for the development of new and innovative bio-products which will be a vital source to build bio and pharmaceutical industries, including aquaculture. In recent years, attempts have been made to discover the chemical ingredients present in these microbes in the form of biomolecules/bioactive compounds with their functions and usefulness for various health benefits, particularly for the treatment of different types of disorders in animals. Therefore, it has been speculated that microbiomes hold great promise not only as a cure for ailments but also as a preventive measure for the number of infectious diseases. This kind of exploration of new breeds of microbes with their miraculous ingredients will definitely help to accelerate the development of the drugs, pharmaceutical and other biological related industries. Probiotic research and bioinformatics skills will further escalate these opportunities in the sector. In the present review, efforts have been made to collect comprehensive information on the finfish and shellfish microbiome, their diversity and functional properties, relationship with diseases, health status, data on species-specific metagenomics, probiotic research and bioinformatics skills. Further, emphasis has also been made to carry out microbiome research on priority basis not only to keep healthy environment of the fish farming sector but also for the sustainable growth of biological related industries, including aquaculture.
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Affiliation(s)
- Arvind D Diwan
- Mahatma Gandhi Mission's (MGM) Institute of Biosciences and Technology, MGM University, Aurangabad, Maharashtra, India
| | - Sanjay N Harke
- Mahatma Gandhi Mission's (MGM) Institute of Biosciences and Technology, MGM University, Aurangabad, Maharashtra, India
| | - Gopalkrishna
- Central Institute of Fisheries Education (CIFE, Deemed University), ICAR, Mumbai, India
| | - Archana N Panche
- Mahatma Gandhi Mission's (MGM) Institute of Biosciences and Technology, MGM University, Aurangabad, Maharashtra, India
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Lim SY, Loo KW, Wong WL. Synergistic Antimicrobial Effect of a Seaweed-Probiotic Blend Against Acute Hepatopancreatic Necrosis Disease (AHPND)-Causing Vibrio parahaemolyticus. Probiotics Antimicrob Proteins 2021; 12:906-917. [PMID: 31773414 DOI: 10.1007/s12602-019-09616-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The outbreak of acute hepatopancreatic necrosis disease (AHPND) has caused great economic losses to the shrimp culture sector. However, the use of antibiotics to fight this disease has resulted in negative impacts on human health and the environment. Thus, the use of natural alternatives to antibiotics may be a better solution. In this study, four Bacillus species obtained from the guts of shrimps (Fenneropenaeus penicillatus and Penaeus monodon) showed antimicrobial activity against the AHPND-causing Vibrio parahaemolyticus strain 3HP using the cross-streaking and agar spot methods. Two of the Bacillus isolates, B2 and BT, also showed good probiotic properties, exhibiting tolerance to bile, good adhesion to shrimp mucus, non-hemolytic, susceptibility to antibiotics and being safe towards hosts. Moreover, a seaweed-probiotic blend (a combination of Bacillus B2 and 20 mg/ml of the red seaweed Gracilaria sp.) exhibited synergistic in vitro inhibition against V. parahaemolyticus strain 3HP, with an observed inhibition zone of 5.0 mm. The broth co-culture experiment results further indicated that the seaweed-probiotic blend inhibited V. parahaemolyticus through competitive exclusion. The in vivo challenge trials also confirmed that this seaweed-probiotic blend significantly reduced the mortality of shrimps post-challenge with the AHPND-causing V. parahaemolyticus strain 3HP (p < 0.05) compared to the negative control (mortality rate = 13.88% vs 72.19%). Thus, this seaweed-probiotic blend may serve as an alternative to antibiotics in controlling the outbreak of AHPND.
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Affiliation(s)
- Shen-Yin Lim
- Department of Biological Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900, Kampar, Perak, Malaysia
| | - Keat Wei Loo
- Department of Biological Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900, Kampar, Perak, Malaysia
| | - Wey-Lim Wong
- Department of Biological Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900, Kampar, Perak, Malaysia.
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16
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Jagannathan SV, Manemann EM, Rowe SE, Callender MC, Soto W. Marine Actinomycetes, New Sources of Biotechnological Products. Mar Drugs 2021; 19:365. [PMID: 34201951 PMCID: PMC8304352 DOI: 10.3390/md19070365] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/14/2021] [Accepted: 06/21/2021] [Indexed: 02/07/2023] Open
Abstract
The Actinomycetales order is one of great genetic and functional diversity, including diversity in the production of secondary metabolites which have uses in medical, environmental rehabilitation, and industrial applications. Secondary metabolites produced by actinomycete species are an abundant source of antibiotics, antitumor agents, anthelmintics, and antifungals. These actinomycete-derived medicines are in circulation as current treatments, but actinomycetes are also being explored as potential sources of new compounds to combat multidrug resistance in pathogenic bacteria. Actinomycetes as a potential to solve environmental concerns is another area of recent investigation, particularly their utility in the bioremediation of pesticides, toxic metals, radioactive wastes, and biofouling. Other applications include biofuels, detergents, and food preservatives/additives. Exploring other unique properties of actinomycetes will allow for a deeper understanding of this interesting taxonomic group. Combined with genetic engineering, microbial experimental evolution, and other enhancement techniques, it is reasonable to assume that the use of marine actinomycetes will continue to increase. Novel products will begin to be developed for diverse applied research purposes, including zymology and enology. This paper outlines the current knowledge of actinomycete usage in applied research, focusing on marine isolates and providing direction for future research.
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Affiliation(s)
| | | | | | | | - William Soto
- Department of Biology, College of William & Mary, Williamsburg, VA 23185, USA; (S.V.J.); (E.M.M.); (S.E.R.); (M.C.C.)
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17
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Characterization of Streptomyces Isolates Associated with Estuarine Fish Chanos chanos and Profiling of Their Antibacterial Metabolites-Crude-Extract. Int J Microbiol 2020; 2020:8851947. [PMID: 33029146 PMCID: PMC7530512 DOI: 10.1155/2020/8851947] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/12/2020] [Indexed: 11/18/2022] Open
Abstract
Streptomyces has been reported as an essential producer of bioactive substances, including antibiotics and other types of antimicrobials. This study investigated antibacterial-producing Streptomyces isolated from the gut of estuarine fish Chanos chanos, emphasizing screening for the producer of peptide-containing antibacterial compounds. Eighteen isolates were found during preliminary screening, in which four isolates showed the best antibacterial activities. Based on the morphological, physiological, and biochemical characterization, as well as 16S rRNA partial sequencing, all of the four isolates belonged to Streptomyces. Three isolates were suspected as novel isolate candidates based on homology presentations and phylogenetic tree analysis. Disk-diffusion assay of the metabolite-crude-extract from the isolates showed broad-spectrum inhibitory activities against Staphylococcus aureus ATCC 25923, Bacillus cereus ATCC 10876, Escherichia coli ATCC 25922, and Pseudomonas aeruginosa InaCC B52 with minimum inhibitory concentration and minimum bactericidal concentration ranging from 2.5-10 mg/mL and 5-10 mg/mL, respectively. The highest antibacterial activity with low MIC and MBC values was shown by isolate AIA-10. Qualitative HPLC profiling revealed that the metabolic-crude-extracts showed many peaks with intensive area at 210 and 214 nm, especially from SCA-11 and AIA-10, indicating the presence of peptide groups in the structure of the constituent compound. The results also suggested that crude extracts SCA-11 and AIA-10 had higher hydrophobicity properties than the other extracts. Further characterization of the active compound was needed to find out which compounds were responsible for the antibacterial activity. The results of this study indicated that some Streptomyces isolated from new environmental niches, i.e., gut of estuarine fish Chanos chanos, produce promising peptide-containing bioactive compounds.
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18
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The intestine of artificially bred larval turbot (Scophthalmus maximus) contains a stable core group of microbiota. Arch Microbiol 2020; 202:2619-2628. [PMID: 32691103 DOI: 10.1007/s00203-020-01984-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/23/2020] [Accepted: 07/14/2020] [Indexed: 02/08/2023]
Abstract
Generally speaking, fish intestinal microbiota is easily affected by food or water environment, and it may be dynamically changed along with body growth. However, it remains unclear whether fish gut microbiota can be affected under any conditions. In the present study, we focused on cultured larval turbot (Scophthalmus maximus) and tracked its artificial breeding process from eggs to larvae in two farms located in different regions of China. Through continuous sampling, we analyzed and compared characteristics of intestinal microbiota in turbot larvae and its correlation with the bacteria in water and food at different developmental stages. The results showed that there was a steady group of microbiota in larval gut, and the highest relative abundance of strain was same between the two farms. This microbiota was established soon after hatching of fertilized eggs. Particularly, the structure of this microbiota was nearly not changeable afterward 3-4 months of development. The bacteria carried by fertilized eggs might play an important role during the formation of this microbiota. In conclusion, our findings suggested that there was a core microbiota represented by Lactococcus sp. in gut of artificially bred turbot larvae. The relative proportion of such strain in gut was higher than 30% at the initial stage of turbot life.
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19
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Condren AR, Costa MS, Sanchez NR, Konkapaka S, Gallik KL, Saxena A, Murphy BT, Sanchez LM. Addition of insoluble fiber to isolation media allows for increased metabolite diversity of lab-cultivable microbes derived from zebrafish gut samples. Gut Microbes 2020; 11:1064-1076. [PMID: 32202200 PMCID: PMC7524352 DOI: 10.1080/19490976.2020.1740073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
There is a gap in measured microbial diversity when comparing genomic sequencing techniques versus cultivation from environmental samples in a laboratory setting. Standardized methods in artificial environments may not recapitulate the environmental conditions that native microbes require for optimal growth. For example, the intestinal tract houses microbes at various pH values as well as minimal oxygen and light environments. These microbes are also exposed to an atypical source of carbon: dietary fiber compacted in fecal matter. To investigate how the addition of insoluble fiber to isolation media could affect the cultivation of microbes from zebrafish intestines, an isolate library was built and analyzed using the bioinformatics pipeline IDBac. While all isolation media encouraged the growth of species from several phyla, the extent of growth was greater with the addition of fiber allowing for easier isolation. Furthermore, fiber addition altered the metabolism of the cultivated gut-derived microbes and induced the production of unique metabolites that were not produced when microbes were otherwise grown on standard isolation media. Addition of this inexpensive carbon source to the media supported the cultivation of a diverse community whose secondary metabolite production may more closely replicate their metabolite production in vivo.
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Affiliation(s)
- Alanna R. Condren
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Maria S Costa
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA,Faculty of Pharmaceutical Sciences, University of Iceland, Reykjavik, Iceland
| | - Natalia Rivera Sanchez
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Sindhu Konkapaka
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Kristin L Gallik
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Ankur Saxena
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Brian T Murphy
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Laura M Sanchez
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA,CONTACT Laura M Sanchez Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL60612, USA
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20
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Reverter M, Sasal P, Suzuki MT, Raviglione D, Inguimbert N, Pare A, Banaigs B, Voisin SN, Bulet P, Tapissier-Bontemps N. Insights into the Natural Defenses of a Coral Reef Fish Against Gill Ectoparasites: Integrated Metabolome and Microbiome Approach. Metabolites 2020; 10:E227. [PMID: 32486312 PMCID: PMC7345202 DOI: 10.3390/metabo10060227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/22/2020] [Accepted: 05/29/2020] [Indexed: 12/21/2022] Open
Abstract
Understanding natural defense mechanisms against parasites can be a valuable tool for the development of innovative therapies. We have previously identified a butterflyfish species (Chaetodon lunulatus) that avoids gill monogenean parasites while living amongst closely related parasitized species. The metabolome and microbiome of several sympatric butterflyfish species from the island of Moorea (French Polynesia) were previously described. In this study, we used the previously generated datasets in an attempt to identify metabolites and bacteria potentially involved in parasite defense mechanisms. We investigated the interplay between the gill mucus metabolome and microbiome of the non-susceptible C. lunulatus versus sympatric butterflyfish species that were always found parasitized in the Central and Eastern Indo-Pacific. After observing significant differences between the metabolome and bacteria of susceptible versus non-susceptible fish, we obtained the discriminant metabolites and operational taxonomic units (OTUs) using a supervised analysis. Some of the most important discriminant metabolites were identified as peptides, and three new peptides derived from β-subunit hemoglobin from C. lunulatus (CLHbβ-1, CLHbβ-2, and CLHbβ-3) were purified, characterized and synthesized to confirm their structures. We also identified specific bacterial families and OTUs typical from low-oxygen habitats in C. lunulatus gill mucus. By using a correlation network between the two datasets, we found a Fusobacteriaceae strain exclusively present in C. lunulatus and highly correlated to the peptides. Finally, we discuss the possible involvement of these peptides and Fusobacteriaceae in monogenean avoidance by this fish species.
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Affiliation(s)
- Miriam Reverter
- Institut für Chemie und Biologie des Meeres, Carl von Ossietzky Universität Oldenburg, 26382 Wilhelmshaven, Germany
- CRIOBE, USR3278-EPHE/CNRS/UPVD/PSL, University of Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan, France; (P.S.); (D.R.); (N.I.); (A.P.); (B.B.)
- Laboratoire d’Excellence ‘CORAIL’, Moorea 98729, French Polynesia
| | - Pierre Sasal
- CRIOBE, USR3278-EPHE/CNRS/UPVD/PSL, University of Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan, France; (P.S.); (D.R.); (N.I.); (A.P.); (B.B.)
- Laboratoire d’Excellence ‘CORAIL’, Moorea 98729, French Polynesia
| | - Marcelino T. Suzuki
- Laboratoire de Biodiversité et Biotechnologies Microbiennes, Sorbonne Université, CNRS, USR3579, Observatoire Océanologique, 66650 Banyuls-sur-mer, France;
| | - Delphine Raviglione
- CRIOBE, USR3278-EPHE/CNRS/UPVD/PSL, University of Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan, France; (P.S.); (D.R.); (N.I.); (A.P.); (B.B.)
| | - Nicolas Inguimbert
- CRIOBE, USR3278-EPHE/CNRS/UPVD/PSL, University of Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan, France; (P.S.); (D.R.); (N.I.); (A.P.); (B.B.)
- Laboratoire d’Excellence ‘CORAIL’, Moorea 98729, French Polynesia
| | - Alan Pare
- CRIOBE, USR3278-EPHE/CNRS/UPVD/PSL, University of Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan, France; (P.S.); (D.R.); (N.I.); (A.P.); (B.B.)
| | - Bernard Banaigs
- CRIOBE, USR3278-EPHE/CNRS/UPVD/PSL, University of Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan, France; (P.S.); (D.R.); (N.I.); (A.P.); (B.B.)
- Laboratoire d’Excellence ‘CORAIL’, Moorea 98729, French Polynesia
| | - Sébastien N. Voisin
- Plateforme BioPark d’Archamps, ArchParc, 74160 Archamps, France; (S.N.V.); (P.B.)
| | - Philippe Bulet
- Plateforme BioPark d’Archamps, ArchParc, 74160 Archamps, France; (S.N.V.); (P.B.)
- CR UGA, IAB, InsermU1209, CNRS UMR 5309, 38700 La Tronche, France
| | - Nathalie Tapissier-Bontemps
- CRIOBE, USR3278-EPHE/CNRS/UPVD/PSL, University of Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan, France; (P.S.); (D.R.); (N.I.); (A.P.); (B.B.)
- Laboratoire d’Excellence ‘CORAIL’, Moorea 98729, French Polynesia
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21
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Condren AR, Kahl LJ, Boelter G, Kritikos G, Banzhaf M, Dietrich LEP, Sanchez LM. Biofilm Inhibitor Taurolithocholic Acid Alters Colony Morphology, Specialized Metabolism, and Virulence of Pseudomonas aeruginosa. ACS Infect Dis 2020; 6:603-612. [PMID: 31851822 DOI: 10.1021/acsinfecdis.9b00424] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Biofilm inhibition by exogenous molecules has been an attractive strategy for the development of novel therapeutics. We investigated the biofilm inhibitor taurolithocholic acid (TLCA) and its effects on the specialized metabolism, virulence, and biofilm formation of the clinically relevant bacterium Pseudomonas aeruginosa strain PA14. Our study shows that TLCA alters the specialized metabolism, thereby affecting P. aeruginosa colony biofilm physiology. We observed an upregulation of metabolites correlated to virulence such as the siderophore pyochelin. A wax moth virulence assay confirmed that treatment with TLCA increases the virulence of P. aeruginosa. On the basis of our results, we believe that future endeavors to identify biofilm inhibitors must consider how a putative lead alters the specialized metabolism of a bacterial community to prevent pathogens from entering a highly virulent state.
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Affiliation(s)
- Alanna R. Condren
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Lisa Juliane Kahl
- Department of Biological Sciences, Columbia University, 617 Fairchild Center, New York, New York 10027, United States
| | - Gabriela Boelter
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - George Kritikos
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Manuel Banzhaf
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Lars E. P. Dietrich
- Department of Biological Sciences, Columbia University, 617 Fairchild Center, New York, New York 10027, United States
| | - Laura M. Sanchez
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
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22
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Barnes EM, Carter EL, Lewis JD. Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa. Front Microbiol 2020; 11:101. [PMID: 32117131 PMCID: PMC7018939 DOI: 10.3389/fmicb.2020.00101] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/17/2020] [Indexed: 12/30/2022] Open
Abstract
Variation in the microbiome among individual organisms may play a critical role in the relative susceptibility of those organisms to infection, disease, and death. However, predicting microbiome function is difficult because of spatial and temporal variation in microbial diversity, and taxonomic diversity is not predictive of microbiome functional diversity. Addressing this issue may be particularly important when addressing pandemic diseases, such as the global amphibian die-off associated with Bd. Some of the most important factors in probiotic development for disease treatment are whether bacteria with desired function can be found on native amphibians in the local environment. To address this issue, we isolated, sequenced, and assayed the cutaneous bacterial communities of Plethodon cinereus along a gradient of land use change. Our results suggest that cutaneous community composition, but not overall diversity, change with changes in land use, but this does not correspond to significant change in Bd-inhibitory function. We found that Bd-inhibition is a functionally redundant trait, but that level of inhibition varies over phylogenetic, spatial, and temporal scales. This research provides further evidence for the importance of continued examination of amphibian microbial communities across environmental gradients, including biotic and abiotic interactions, when considering disease dynamics.
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Affiliation(s)
- Elle M Barnes
- Department of Biological Sciences, Louis Calder Center - Biological Field Station, Fordham University, Armonk, NY, United States.,Department of Biological Sciences and Center for Urban Ecology, Fordham University, Bronx, NY, United States
| | - Erin L Carter
- Department of Biological Sciences and Center for Urban Ecology, Fordham University, Bronx, NY, United States
| | - J D Lewis
- Department of Biological Sciences, Louis Calder Center - Biological Field Station, Fordham University, Armonk, NY, United States.,Department of Biological Sciences and Center for Urban Ecology, Fordham University, Bronx, NY, United States
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23
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Johny TK, Saidumohamed BE, Sasidharan RS, Bhat SG. Inferences of gut bacterial diversity from next-generation sequencing of 16S rDNA in deep sea blind ray - Benthobatis moresbyi. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.egg.2018.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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24
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Abstract
Fish mucus layers are the main surface of exchange between fish and the environment, and they possess important biological and ecological functions. Fish mucus research is increasing rapidly, along with the development of high-throughput techniques, which allow the simultaneous study of numerous genes and molecules, enabling a deeper understanding of the fish mucus composition and its functions. Fish mucus plays a major role against fish infections, and research has mostly focused on the study of fish mucus bioactive molecules (e.g., antimicrobial peptides and immune-related molecules) and associated microbiota due to their potential in aquaculture and human medicine. However, external fish mucus surfaces also play important roles in social relationships between conspecifics (fish shoaling, spawning synchronisation, suitable habitat finding, or alarm signals) and in interspecific interactions such as prey-predator relationships, parasite–host interactions, and symbiosis. This article reviews the biological and ecological roles of external (gills and skin) fish mucus, discussing its importance in fish protection against pathogens and in intra and interspecific interactions. We also discuss the advances that “omics” sciences are bringing into the fish mucus research and their importance in studying the fish mucus composition and functions.
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25
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Jones J, DiBattista JD, Stat M, Bunce M, Boyce MC, Fairclough DV, Travers MJ, Huggett MJ. The Microbiome of the Gastrointestinal Tract of a Range-Shifting Marine Herbivorous Fish. Front Microbiol 2018; 9:2000. [PMID: 30210475 PMCID: PMC6121097 DOI: 10.3389/fmicb.2018.02000] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/08/2018] [Indexed: 01/01/2023] Open
Abstract
Globally, marine species’ distributions are being modified due to rising ocean temperatures. Increasing evidence suggests a circum-global pattern of poleward extensions in the distributions of many tropical herbivorous species, including the ecologically important rabbitfish Siganus fuscescens. Adaptability of a species to such new environments may be heavily influenced by the composition of their gastrointestinal microbe fauna, which is fundamentally important to animal health. Siganus fuscescens thus provides an opportunity to assess the stability of gastrointestinal microbes under varying environmental conditions. The gastrointestinal microbial communities of S. fuscescens were characterized over 2,000 km of Australia’s western coast, from tropical to temperate waters, including near its current southern distributional limit. Sequencing of the 16S rRNA gene demonstrated that each population had a distinct hindgut microbial community, and yet, 20 OTUs occurred consistently in all samples. These OTUs were considered the ‘core microbiome’ and were highly abundant, composing between 31 and 54% of each population. Furthermore, levels of short chain fatty acids, an indicator of microbial fermentation activity, were similar among tropical and temperate locations. These data suggest that flexibility in the hindgut microbiome may play a role in enabling such herbivores to colonize new environments beyond their existing range.
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Affiliation(s)
- Jacquelyn Jones
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Joseph D DiBattista
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth WA, Australia.,Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Michael Stat
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth WA, Australia.,Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth WA, Australia
| | - Mary C Boyce
- Centre for Ecosystem Management, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - David V Fairclough
- Department of Primary Industries and Regional Development, Fisheries Division, Government of Western Australia, Hillarys, WA, Australia
| | - Michael J Travers
- Department of Primary Industries and Regional Development, Fisheries Division, Government of Western Australia, Hillarys, WA, Australia
| | - Megan J Huggett
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, WA, Australia.,Centre for Ecosystem Management, School of Science, Edith Cowan University, Joondalup, WA, Australia.,School of Environmental and Life Sciences, University of Newcastle, Ourimbah, NSW, Australia
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26
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Zhang H, Tang H, Zang Y, Tang X, Wang Y. Microorganism's adaptation of Crucian carp may closely relate to its living environments. Microbiologyopen 2018; 8:e00650. [PMID: 29877059 PMCID: PMC6436428 DOI: 10.1002/mbo3.650] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/07/2018] [Accepted: 04/07/2018] [Indexed: 11/16/2022] Open
Abstract
The relationship between the internal microbiome of an individual organism and that of its external environment has been little investigated in freshwater ecosystems. Thus, this is an area of interest in freshwater fish biology. Along with the genotype of the fish host, external environment plays an important role in determining the composition of the internal microbiome. Here, we characterized the variability of the microbiome of wild Crucian carp (Carassius auratus), along with those of their surrounding environments (water and mud). We found that each environment had distinct bacterial communities, with varying composition and structure. The primary bacterial phyla identified in the Crucian carp gut were Fusobacteria and Proteobacteria (90% of all bacterial phyla identified); the primary genera identified were Cetobacterium, Aeromonas, and Plesiomonas (85% of all bacterial phyla identified). We identified 1,739 operational taxonomic units (OTUs) in the Crucian carp gut, 1,703 in water, and 5,322 in mud. Each environment had unique OTUs, but the fewest unique OTUs (97) were found in the Crucian carp gut. There were significant differences in the relative abundances of different bacterial phyla in the different environments. It may be that only bacterial phyla vital for efficient fish function (e.g., immune response or metabolism), such as Fusobacteria and Proteobacteria, are retained in the Crucian carp gut.
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Affiliation(s)
- Huanxin Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hongshuo Tang
- College of Information Science and Engineering, Ocean University of China, Qingdao, China
| | - Yu Zang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ying Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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27
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Warner CJA, Salinas M, Zamorano-Sánchez D, Bray WM, Lokey RS, Yildiz FH, Linington RG. The Bioactive Lipid (S)-Sebastenoic Acid Impacts Motility and Dispersion in Vibrio cholerae. CAN J CHEM 2018; 96:196-203. [PMID: 34158674 DOI: 10.1139/cjc-2017-0334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Although Gram-negative bacterial pathogens continue to impart a substantial burden on global healthcare systems, much remains to be understood about aspects of basic physiology in these organisms. In recent years, cyclic-diguanylate (c-di-GMP) has emerged as a key regulator of a number of important processes related to pathogenicity, including biofilm formation, motility and virulence. In an effort to discover chemical genetic probes for studying V. cholerae we have developed a new motility-based high-throughput screen to identify compounds that modulate c-di-GMP levels. Using this new screening platform, we tested a library of microbially-derived marine natural products extracts, leading to the discovery of the bioactive lipid (S)-sebastenoic acid. Evaluation of the effect of this new compound on bacterial motility, vpsL expression and biofilm formation implied that (S)-sebastenoic acid may alter phenotypes associated to c-di-GMP signaling in V. cholerae.
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Affiliation(s)
- Christopher J A Warner
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mauro Salinas
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Zamorano-Sánchez
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Walter M Bray
- Chemical Screening Center, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,Chemical Screening Center, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Roger G Linington
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby V5A 1S6, Canada
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28
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Ochoa JL, Sanchez LM, Koo BM, Doherty JS, Rajendram M, Huang KC, Gross CA, Linington RG. Marine Mammal Microbiota Yields Novel Antibiotic with Potent Activity Against Clostridium difficile. ACS Infect Dis 2018; 4:59-67. [PMID: 29043783 DOI: 10.1021/acsinfecdis.7b00105] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The recent explosion of research on the microbiota has highlighted the important interplay between commensal microorganisms and the health of their cognate hosts. Metabolites isolated from commensal bacteria have been demonstrated to possess a range of antimicrobial activities, and it is widely believed that some of these metabolites modulate host behavior, affecting predisposition to disease and pathogen invasion. Our access to the local marine mammal stranding network and previous successes in mining the fish microbiota poised us to test the hypothesis that the marine mammal microbiota is a novel source of commensal bacteria-produced bioactive metabolites. Examination of intestinal contents from five marine mammals led to the identification of a Micromonospora strain with potent and selective activity against a panel of Gram-positive pathogens and no discernible human cytotoxicity. Compound isolation afforded a new complex glycosylated polyketide, phocoenamicin, with potent activity against the intestinal pathogen Clostridium difficile, an organism challenging to treat in hospital settings. Use of our activity-profiling platform, BioMAP, clustered this metabolite with other known ionophore antibiotics. Fluorescence imaging and flow cytometry confirmed that phocoenamicin is capable of shifting membrane potential without damaging membrane integrity. Thus, exploration of gut microbiota in hosts from diverse environments can serve as a powerful strategy for the discovery of novel antibiotics against human pathogens.
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Affiliation(s)
- Jessica L. Ochoa
- Department of Chemistry
and Biochemistry, University of California Santa Cruz, 1156 High
Street, Santa Cruz, California 95064, United States
| | - Laura M. Sanchez
- Department of Chemistry
and Biochemistry, University of California Santa Cruz, 1156 High
Street, Santa Cruz, California 95064, United States
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Byoung-Mo Koo
- Department of Microbiology and Immunology, University of California San Francisco, 600 16th Street, San Francisco, California 94158, United States
| | - Jennifer S. Doherty
- Department of Microbiology and Immunology, University of California San Francisco, 600 16th Street, San Francisco, California 94158, United States
| | - Manohary Rajendram
- Department
of Bioengineering, Stanford University, Shriram Center for Bioengineering and Chemical Engineering, 443 Via Ortega, Stanford, California 94305, United States
| | - Kerwyn Casey Huang
- Department
of Bioengineering, Stanford University, Shriram Center for Bioengineering and Chemical Engineering, 443 Via Ortega, Stanford, California 94305, United States
- Department of Microbiology and Immunology, Stanford University School of Medicine,299 Campus Drive, Stanford, California 94305, United States
| | - Carol A. Gross
- Department of Microbiology and Immunology, University of California San Francisco, 600 16th Street, San Francisco, California 94158, United States
| | - Roger G. Linington
- Department of Chemistry
and Biochemistry, University of California Santa Cruz, 1156 High
Street, Santa Cruz, California 95064, United States
- Department of Chemistry, Simon Fraser University, 8888
University Drive, Burnaby, British Columbia V5A 1S6, Canada
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29
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Reverter M, Sasal P, Tapissier-Bontemps N, Lecchini D, Suzuki M. Characterisation of the gill mucosal bacterial communities of four butterflyfish species: a reservoir of bacterial diversity in coral reef ecosystems. FEMS Microbiol Ecol 2017; 93:3738480. [DOI: 10.1093/femsec/fix051] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 04/17/2017] [Indexed: 12/26/2022] Open
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30
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Motley J, Stamps BW, Mitchell CA, Thompson AT, Cross J, You J, Powell DR, Stevenson BS, Cichewicz RH. Opportunistic Sampling of Roadkill as an Entry Point to Accessing Natural Products Assembled by Bacteria Associated with Non-anthropoidal Mammalian Microbiomes. JOURNAL OF NATURAL PRODUCTS 2017; 80:598-608. [PMID: 28335605 PMCID: PMC5368682 DOI: 10.1021/acs.jnatprod.6b00772] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Indexed: 05/09/2023]
Abstract
Few secondary metabolites have been reported from mammalian microbiome bacteria despite the large numbers of diverse taxa that inhabit warm-blooded higher vertebrates. As a means to investigate natural products from these microorganisms, an opportunistic sampling protocol was developed, which focused on exploring bacteria isolated from roadkill mammals. This initiative was made possible through the establishment of a newly created discovery pipeline, which couples laser ablation electrospray ionization mass spectrometry (LAESIMS) with bioassay testing, to target biologically active metabolites from microbiome-associated bacteria. To illustrate this process, this report focuses on samples obtained from the ear of a roadkill opossum (Dideiphis virginiana) as the source of two bacterial isolates (Pseudomonas sp. and Serratia sp.) that produced several new and known cyclic lipodepsipeptides (viscosin and serrawettins, respectively). These natural products inhibited biofilm formation by the human pathogenic yeast Candida albicans at concentrations well below those required to inhibit yeast viability. Phylogenetic analysis of 16S rRNA gene sequence libraries revealed the presence of diverse microbial communities associated with different sites throughout the opossum carcass. A putative biosynthetic pathway responsible for the production of the new serrawettin analogues was identified by sequencing the genome of the Serratia sp. isolate. This study provides a functional roadmap to carrying out the systematic investigation of the genomic, microbiological, and chemical parameters related to the production of natural products made by bacteria associated with non-anthropoidal mammalian microbiomes. Discoveries emerging from these studies are anticipated to provide a working framework for efforts aimed at augmenting microbiomes to deliver beneficial natural products to a host.
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Affiliation(s)
- Jeremy
L. Motley
- Natural
Products Discovery Group, Department of Chemistry and Biochemistry, and Institute for
Natural Products Applications and Research Technologies, Stephenson
Life Sciences Research Center, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
| | - Blake W. Stamps
- Department
of Microbiology and Plant Biology, University
of Oklahoma, Norman, Oklahoma 73019-0390, United States
| | - Carter A. Mitchell
- Natural
Products Discovery Group, Department of Chemistry and Biochemistry, and Institute for
Natural Products Applications and Research Technologies, Stephenson
Life Sciences Research Center, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
| | - Alec T. Thompson
- Natural
Products Discovery Group, Department of Chemistry and Biochemistry, and Institute for
Natural Products Applications and Research Technologies, Stephenson
Life Sciences Research Center, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
| | - Jayson Cross
- Natural
Products Discovery Group, Department of Chemistry and Biochemistry, and Institute for
Natural Products Applications and Research Technologies, Stephenson
Life Sciences Research Center, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
| | - Jianlan You
- Natural
Products Discovery Group, Department of Chemistry and Biochemistry, and Institute for
Natural Products Applications and Research Technologies, Stephenson
Life Sciences Research Center, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
| | - Douglas R. Powell
- Natural
Products Discovery Group, Department of Chemistry and Biochemistry, and Institute for
Natural Products Applications and Research Technologies, Stephenson
Life Sciences Research Center, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
| | - Bradley S. Stevenson
- Natural
Products Discovery Group, Department of Chemistry and Biochemistry, and Institute for
Natural Products Applications and Research Technologies, Stephenson
Life Sciences Research Center, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
- Department
of Microbiology and Plant Biology, University
of Oklahoma, Norman, Oklahoma 73019-0390, United States
| | - Robert H. Cichewicz
- Natural
Products Discovery Group, Department of Chemistry and Biochemistry, and Institute for
Natural Products Applications and Research Technologies, Stephenson
Life Sciences Research Center, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
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31
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Oetama VSP, Hennersdorf P, Abdul-Aziz MA, Mrotzek G, Haryanti H, Saluz HP. Microbiome analysis and detection of pathogenic bacteria of Penaeus monodon from Jakarta Bay and Bali. MARINE POLLUTION BULLETIN 2016; 110:718-725. [PMID: 27090886 DOI: 10.1016/j.marpolbul.2016.03.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 03/09/2016] [Accepted: 03/20/2016] [Indexed: 06/05/2023]
Abstract
Penaeus monodon, the Asian black tiger shrimp is one of the most widely consumed marine crustaceans worldwide. In this study, we examine and compare the fecal microbiota of P. monodon from highly polluted waters around Jakarta Bay, with those of less polluted waters of Bali. Using next generation sequencing techniques, we identified potential bacterial pathogens and common viral diseases of shrimp. Proteobacteria (96.08%) was found to be the most predominant phylum, followed by Bacteriodetes (2.32%), Fusobacteria (0.96%), and Firmicutes (0.53%). On the order level, Vibrionales (66.20%) and Pseudoaltermonadales (24.81%) were detected as predominant taxa. qPCR profiling was used as a confirmatory step and further revealed Vibrio alginolyticus and Photobacterium damselae as two potential pathogenic species present in most of the samples. In addition, viral diseases for shrimp were discovered among the samples, WSSV in Jakarta free-living samples, YHV in Bali free-living samples and IHHNV in both.
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Affiliation(s)
- Vincensius S P Oetama
- Leibniz-Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, D-07745 Jena, Germany; Friedrich Schiller University of Jena, Fürstengraben 1, D-07743 Jena, Germany
| | - Philipp Hennersdorf
- Leibniz-Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, D-07745 Jena, Germany; Friedrich Schiller University of Jena, Fürstengraben 1, D-07743 Jena, Germany
| | - Muslihudeen A Abdul-Aziz
- Friedrich Schiller University of Jena, Fürstengraben 1, D-07743 Jena, Germany; Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia
| | - Grit Mrotzek
- Leibniz-Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, D-07745 Jena, Germany
| | - Haryanti Haryanti
- Gondol Research Institute for Mariculture GRIM, ds Penyabangan, Br. Gondol, PO. Box 140, Singaraja 81101, Bali, Indonesia
| | - Hans Peter Saluz
- Leibniz-Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, D-07745 Jena, Germany; Friedrich Schiller University of Jena, Fürstengraben 1, D-07743 Jena, Germany
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32
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Giatsis C, Sipkema D, Ramiro-Garcia J, Bacanu GM, Abernathy J, Verreth J, Smidt H, Verdegem M. Probiotic legacy effects on gut microbial assembly in tilapia larvae. Sci Rep 2016; 6:33965. [PMID: 27670882 PMCID: PMC5037425 DOI: 10.1038/srep33965] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/30/2016] [Indexed: 02/08/2023] Open
Abstract
The exposure of fish to environmental free-living microbes and its effect on early colonization in the gut have been studied in recent years. However, little is known regarding how the host and environment interact to shape gut communities during early life. Here, we tested whether the early microbial exposure of tilapia larvae affects the gut microbiota at later life stages. The experimental period was divided into three stages: axenic, probiotic and active suspension. Axenic tilapia larvae were reared either under conventional conditions (active suspension systems) or exposed to a single strain probiotic (Bacillus subtilis) added to the water. Microbial characterization by Illumina HiSeq sequencing of 16S rRNA gene amplicons showed the presence of B. subtilis in the gut during the seven days of probiotic application. Although B. subtilis was no longer detected in the guts of fish exposed to the probiotic after day 7, gut microbiota of the exposed tilapia larvae remained significantly different from that of the control treatment. Compared with the control, fish gut microbiota under probiotic treatment was less affected by spatial differences resulting from tank replication, suggesting that the early probiotic contact contributed to the subsequent observation of low inter-individual variation.
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Affiliation(s)
- Christos Giatsis
- Aquaculture and Fisheries Group, Wageningen University, De Elst 1, 6708 WD Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Javier Ramiro-Garcia
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Laboratory of System and Synthetic Biology, Stippeneng 4, Wageningen 6708 WE, The Netherlands
- TI Food and Nutrition (TIFN) P.O. Box 557, 6700 AN, Wageningen 6703 HB, The Netherlands
| | - Gianina M. Bacanu
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Jason Abernathy
- USDA-ARS, Hagerman Fish Culture Experiment Station, 3059F National Fish Hatchery Road, Hagerman, Idaho 83332, USA
| | - Johan Verreth
- Aquaculture and Fisheries Group, Wageningen University, De Elst 1, 6708 WD Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Marc Verdegem
- Aquaculture and Fisheries Group, Wageningen University, De Elst 1, 6708 WD Wageningen, The Netherlands
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33
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Zolnik CP, Prill RJ, Falco RC, Daniels TJ, Kolokotronis SO. Microbiome changes through ontogeny of a tick pathogen vector. Mol Ecol 2016; 25:4963-77. [DOI: 10.1111/mec.13832] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 08/19/2016] [Accepted: 08/29/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Christine P. Zolnik
- Department of Biological Sciences; Fordham University; 441 East Fordham Road Bronx NY 10458 USA
- Vector Ecology Laboratory; Louis Calder Center-Biological Field Station; Fordham University; 53 Whippoorwill Road Armonk NY 10504 USA
| | - Robert J. Prill
- IBM Almaden Research Center; 650 Harry Road San Jose CA 95120 USA
| | - Richard C. Falco
- New York State Department of Health; Louis Calder Center-Biological Field Station; Fordham University; 53 Whippoorwill Road Armonk NY 10504 USA
| | - Thomas J. Daniels
- Vector Ecology Laboratory; Louis Calder Center-Biological Field Station; Fordham University; 53 Whippoorwill Road Armonk NY 10504 USA
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Gill monogenean communities (Platyhelminthes, Monogenea, Dactylogyridae) of butterflyfishes from tropical Indo-West Pacific Islands. Parasitology 2016; 143:1580-91. [DOI: 10.1017/s0031182016001463] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
SUMMARYWe studied the monogenean communities of 34 species of butterflyfish from the tropical Indo-West Pacific, identifying 13 dactylogyrid species (including two species that are presently undescribed). Monogenean assemblages differed significantly between host species in terms of taxonomic structure, intensity and prevalence. Parasite richness ranged from 0 (Chaetodon lunulatus) to 11 (C. auriga, C. citrinellus and C. lunula). Host specificity varied between the dactylogyrids species, being found on 2–29 of the 34 chaetodontid species examined. Sympatric butterflyfish species were typically parasitized by different combinations of dactylogyrid species, suggesting the existence of complex host–parasite interactions. We identified six clusters of butterflyfish species based on the similarities of their dactylogyrid communities. Dactylogyrid richness and diversity were not related to host size, diet specialization, depth range or phylogeny of butterflyfish species. However, there was a weak positive correlation between monogenean richness and diversity and host geographical range. Most communities of dactylogyrids were dominated by Haliotrema aurigae and H. angelopterum, indicating the importance of the genus Haliotrema in shaping monogenean communities of butterflyfishes. This study casts light on the structure of the monogenean communities of butterflyfishes, suggesting that the diversity and complexity of community structures arises from a combination of host species-specific parameters.
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Abdelrhman KFA, Bacci G, Mancusi C, Mengoni A, Serena F, Ugolini A. A First Insight into the Gut Microbiota of the Sea Turtle Caretta caretta. Front Microbiol 2016; 7:1060. [PMID: 27458451 PMCID: PMC4935691 DOI: 10.3389/fmicb.2016.01060] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 06/23/2016] [Indexed: 11/17/2022] Open
Affiliation(s)
| | - Giovanni Bacci
- Dipartimento di Biologia, Università di Firenze Sesto Fiorentino, Italy
| | - Cecilia Mancusi
- Agenzia Regionale per la Protezione Ambientale della Toscana Livorno, Italy
| | - Alessio Mengoni
- Dipartimento di Biologia, Università di Firenze Sesto Fiorentino, Italy
| | - Fabrizio Serena
- Agenzia Regionale per la Protezione Ambientale della Toscana Livorno, Italy
| | - Alberto Ugolini
- Dipartimento di Biologia, Università di Firenze Sesto Fiorentino, Italy
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Identification, library synthesis and anti-vibriosis activity of 2-benzyl-4-chlorophenol from cultures of the marine bacterium Shewanella halifaxensis. Bioorg Med Chem Lett 2016; 26:3086-3088. [DOI: 10.1016/j.bmcl.2016.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 05/02/2016] [Accepted: 05/03/2016] [Indexed: 12/14/2022]
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Biofilm Formation and Detachment in Gram-Negative Pathogens Is Modulated by Select Bile Acids. PLoS One 2016; 11:e0149603. [PMID: 26992172 PMCID: PMC4798295 DOI: 10.1371/journal.pone.0149603] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 02/03/2016] [Indexed: 11/19/2022] Open
Abstract
Biofilms are a ubiquitous feature of microbial community structure in both natural and host environments; they enhance transmission and infectivity of pathogens and provide protection from human defense mechanisms and antibiotics. However, few natural products are known that impact biofilm formation or persistence for either environmental or pathogenic bacteria. Using the combination of a novel natural products library from the fish microbiome and an image-based screen for biofilm inhibition, we describe the identification of taurine-conjugated bile acids as inhibitors of biofilm formation against both Vibrio cholerae and Pseudomonas aeruginosa. Taurocholic acid (1) was isolated from the fermentation broth of the fish microbiome-derived strain of Rhodococcus erythropolis and identified using standard NMR and MS methods. Screening of the twelve predominant human steroidal bile acid components revealed that a subset of these compounds can inhibit biofilm formation, induce detachment of preformed biofilms under static conditions, and that these compounds display distinct structure-activity relationships against V. cholerae and P. aeruginosa. Our findings highlight the significance of distinct bile acid components in the regulation of biofilm formation and dispersion in two different clinically relevant bacterial pathogens, and suggest that the bile acids, which are endogenous mammalian metabolites used to solubilize dietary fats, may also play a role in maintaining host health against bacterial infection.
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Ou YX, Huang JF, Li XM, Kang QJ, Pan YT. Three new 2,5-diketopiperazines from the fish intestinal Streptomyces sp. MNU FJ-36. Nat Prod Res 2016; 30:1771-5. [DOI: 10.1080/14786419.2015.1137570] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Yi-xin Ou
- Engineering Technological Center of Mushroom Industry, Minnan Normal University, Zhangzhou, P.R. China
- College of Life Sciences and Technology, Minnan Normal University, Zhangzhou, P.R. China
| | - Jia-fu Huang
- Engineering Technological Center of Mushroom Industry, Minnan Normal University, Zhangzhou, P.R. China
- College of Life Sciences and Technology, Minnan Normal University, Zhangzhou, P.R. China
| | - Xiu-min Li
- Engineering Technological Center of Mushroom Industry, Minnan Normal University, Zhangzhou, P.R. China
- College of Life Sciences and Technology, Minnan Normal University, Zhangzhou, P.R. China
| | - Qian-jin Kang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Yu-tian Pan
- Engineering Technological Center of Mushroom Industry, Minnan Normal University, Zhangzhou, P.R. China
- College of Life Sciences and Technology, Minnan Normal University, Zhangzhou, P.R. China
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Giatsis C, Sipkema D, Smidt H, Heilig H, Benvenuti G, Verreth J, Verdegem M. The impact of rearing environment on the development of gut microbiota in tilapia larvae. Sci Rep 2015; 5:18206. [PMID: 26658351 PMCID: PMC4676014 DOI: 10.1038/srep18206] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 11/13/2015] [Indexed: 02/08/2023] Open
Abstract
This study explores the effect of rearing environment on water bacterial communities (BC) and the association with those present in the gut of Nile tilapia larvae (Oreochromis niloticus, Linnaeus) grown in either recirculating or active suspension systems. 454 pyrosequencing of PCR-amplified 16S rRNA gene fragments was applied to characterize the composition of water, feed and gut bacteria communities. Observed changes in water BC over time and differences in water BCs between systems were highly correlated with corresponding water physico-chemical properties. Differences in gut bacterial communities during larval development were correlated with differences in water communities between systems. The correlation of feed BC with those in the gut was minor compared to that between gut and water, reflected by the fact that 4 to 43 times more OTUs were shared between water and gut than between gut and feed BC. Shared OTUs between water and gut suggest a successful transfer of microorganisms from water into the gut, and give insight about the niche and ecological adaptability of water microorganisms inside the gut. These findings suggest that steering of gut microbial communities could be possible through water microbial management derived by the design and functionality of the rearing system.
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Affiliation(s)
- Christos Giatsis
- Aquaculture and Fisheries Group, Wageningen University, PO Box 338, 6708 WD Wageningen, the Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Hans Heilig
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Giulia Benvenuti
- Bioprocess Engineering, AlgaePARC, Wageningen University, PO Box 16, 6700 AA Wageningen, the Netherlands
| | - Johan Verreth
- Aquaculture and Fisheries Group, Wageningen University, PO Box 338, 6708 WD Wageningen, the Netherlands
| | - Marc Verdegem
- Aquaculture and Fisheries Group, Wageningen University, PO Box 338, 6708 WD Wageningen, the Netherlands
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Topographical Mapping of the Rainbow Trout (Oncorhynchus mykiss) Microbiome Reveals a Diverse Bacterial Community with Antifungal Properties in the Skin. Appl Environ Microbiol 2015. [PMID: 26209676 DOI: 10.1128/aem.01826-15] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The mucosal surfaces of wild and farmed aquatic vertebrates face the threat of many aquatic pathogens, including fungi. These surfaces are colonized by diverse symbiotic bacterial communities that may contribute to fight infection. Whereas the gut microbiome of teleosts has been extensively studied using pyrosequencing, this tool has rarely been employed to study the compositions of the bacterial communities present on other teleost mucosal surfaces. Here we provide a topographical map of the mucosal microbiome of an aquatic vertebrate, the rainbow trout (Oncorhynchus mykiss). Using 16S rRNA pyrosequencing, we revealed novel bacterial diversity at each of the five body sites sampled and showed that body site is a strong predictor of community composition. The skin exhibited the highest diversity, followed by the olfactory organ, gills, and gut. Flectobacillus was highly represented within skin and gill communities. Principal coordinate analysis and plots revealed clustering of external sites apart from internal sites. A highly diverse community was present within the epithelium, as demonstrated by confocal microscopy and pyrosequencing. Using in vitro assays, we demonstrated that two Arthrobacter sp. skin isolates, a Psychrobacter sp. strain, and a combined skin aerobic bacterial sample inhibit the growth of Saprolegnia australis and Mucor hiemalis, two important aquatic fungal pathogens. These results underscore the importance of symbiotic bacterial communities of fish and their potential role for the control of aquatic fungal diseases.
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Lazado CC, Caipang CMA, Estante EG. Prospects of host-associated microorganisms in fish and penaeids as probiotics with immunomodulatory functions. FISH & SHELLFISH IMMUNOLOGY 2015; 45:2-12. [PMID: 25703713 DOI: 10.1016/j.fsi.2015.02.023] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 02/08/2015] [Accepted: 02/12/2015] [Indexed: 05/20/2023]
Abstract
Aquatic animals harbor a great number of microorganisms with interesting biological and biochemical diversity. Besides serving as the natural defense system of the host, the utilization potential of this microbial association has been identified particularly as reservoirs of candidate probiotics. Host-derived probiotics have gained popularity in recent years as they offer an alternative source of beneficial microbes to the industry that is customarily dependent on the use of terrestrial microorganisms. At present, there is an overwhelming number of candidate probiotics in aquaculture but their large-scale application is restricted by bio-technological concerns and fragmentary documented probiotic actions. This paper presents the current understanding on the use of probiotics as a sustainable alternative that promotes health and welfare in fish and penaeids. In particular, this paper discusses the relevance of host microbiota and its potential as a source of candidate probiotics. It also revisits the interaction between probiotics and host immunity to provide the foundation of the immunomodulatory functions of host-derived probiotics. Several studies demonstrating the immunomodulatory capabilities of host-derived candidate probiotics are given to establish the current knowledge and provide avenues for future research and development in this thematic area of probiotics research in aquaculture.
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Affiliation(s)
- Carlo C Lazado
- Section for Aquaculture, National Institute of Aquatic Resources, Technical University of Denmark, North Sea Science Park, 9850, Hirtshals, Denmark.
| | | | - Erish G Estante
- Institute of Aquaculture, College of Fisheries and Ocean Sciences, University of the Philippines Visayas, 5023 Miagao, Iloilo, Philippines
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Bernal MG, Campa-Córdova ÁI, Saucedo PE, González MC, Marrero RM, Mazón-Suástegui JM. Isolation and in vitro selection of actinomycetes strains as potential probiotics for aquaculture. Vet World 2015; 8:170-6. [PMID: 27047067 PMCID: PMC4774698 DOI: 10.14202/vetworld.2015.170-176] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/25/2014] [Accepted: 01/03/2015] [Indexed: 01/14/2023] Open
Abstract
AIM This study was designed to describe a series of in vitro tests that may aid the discovery of probiotic strains from actinomycetes. MATERIALS AND METHODS Actinomycetes were isolated from marine sediments using four different isolation media, followed by antimicrobial activity and toxicity assessment by the agar diffusion method and the hemolysis of human blood cells, respectively. Extracellular enzymatic production was monitored by the hydrolysis of proteins, lipids and carbohydrates. Tolerance to different pH values and salt concentrations was also determined, followed by hydrophobicity analysis and genetic identification of the most promising strains. RESULTS Five out of 31 isolated strains showed antimicrobial activity against three Vibrio species. Three non-hemolytic strains (N7, RL8 and V4) among these active isolates yielded positive results in hydrophobicity tests and exhibited good growth at salt concentrations ranging from 0% to 10%, except strain RL8, which required a salt concentration >0.6%. Although these strains did not grow at pH<3, they showed different enzymatic activities. Phylogenetic analysis revealed that strains N7 and V4 have more than 99% identity with several Streptomyces species, whereas the closest matches to strain RL8 are Streptomyces panacagri and Streptomyces flocculus, with 98% and 98.2% similarity, respectively. CONCLUSION Three actinomycetes strains showing probiotic-like properties were discovered using several in vitro tests that can be easily implemented in different institutions around the world.
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Affiliation(s)
- Milagro García Bernal
- Department of Microbiology, Center for the Study of Bioactive Chemicals (CBQ), Central University “Marta Abreu” of Las Villas. Road to Camajuaní Km 5½. Santa Clara 54830. Villa Clara. Cuba
| | - Ángel Isidro Campa-Córdova
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita Sur, C.P. 23090. La Paz, Baja California Sur, México
| | - Pedro Enrique Saucedo
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita Sur, C.P. 23090. La Paz, Baja California Sur, México
| | - Marlen Casanova González
- Department of Microbiology, Center for the Study of Bioactive Chemicals (CBQ), Central University “Marta Abreu” of Las Villas. Road to Camajuaní Km 5½. Santa Clara 54830. Villa Clara. Cuba
| | - Ricardo Medina Marrero
- Department of Microbiology, Center for the Study of Bioactive Chemicals (CBQ), Central University “Marta Abreu” of Las Villas. Road to Camajuaní Km 5½. Santa Clara 54830. Villa Clara. Cuba
| | - José Manuel Mazón-Suástegui
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita Sur, C.P. 23090. La Paz, Baja California Sur, México
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Jami M, Ghanbari M, Kneifel W, Domig KJ. Phylogenetic diversity and biological activity of culturable Actinobacteria isolated from freshwater fish gut microbiota. Microbiol Res 2015; 175:6-15. [PMID: 25662514 DOI: 10.1016/j.micres.2015.01.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Revised: 01/14/2015] [Accepted: 01/18/2015] [Indexed: 01/25/2023]
Abstract
The diversity of Actinobacteria isolated from the gut microbiota of two freshwater fish species namely Schizothorax zarudnyi and Schizocypris altidorsalis was investigated employing classical cultivation techniques, repetitive sequence-based PCR (rep-PCR), partial and full 16S rDNA sequencing followed by phylogenetic analysis. A total of 277 isolates were cultured by applying three different agar media. Based on rep-PCR profile analysis a subset of 33 strains was selected for further phylogenetic investigations, antimicrobial activity testing and diversity analysis of secondary-metabolite biosynthetic genes. The identification based on 16S rRNA gene sequencing revealed that the isolates belong to eight genera distributed among six families. At the family level, 72% of the 277 isolates belong to the family Streptomycetaceae. Among the non-streptomycetes group, the most dominant group could be allocated to the family of Pseudonocardiaceae followed by the members of Micromonosporaceae. Phylogenetic analysis clearly showed that many of the isolates in the genera Streptomyces, Saccharomonospora, Micromonospora, Nocardiopsis, Arthrobacter, Kocuria, Microbacterium and Agromyces formed a single and distinct cluster with the type strains. Notably, there is no report so far about the occurrence of these Actinobacteria in the microbiota of freshwater fish. Of the 33 isolates, all the strains exhibited antibacterial activity against a set of tested human and fish pathogenic bacteria. Then, to study their associated potential capacity to synthesize diverse bioactive natural products, diversity of genes associated with secondary-metabolite biosynthesis including PKS I, PKS II, NRPS, the enzyme PhzE of the phenazine pathways, the enzyme dTGD of 6-deoxyhexoses glycosylation pathway, the enzyme Halo of halogenation pathway and the enzyme CYP in polyene polyketide biosynthesis were investigated among the isolates. All the strains possess at least two types of the investigated biosynthetic genes, one-fourth of them harbours more than four. This study demonstrates the significant diversity of Actinobacteria in the fish gut microbiota and it's potential to produce biologically active compounds.
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Affiliation(s)
- Mansooreh Jami
- BOKU - University of Natural Resources and Life Sciences, Department of Food Science and Technology, Institute of Food Science, Muthgasse 18, A-1190 Vienna, Austria.
| | - Mahdi Ghanbari
- BOKU - University of Natural Resources and Life Sciences, Department of Food Science and Technology, Institute of Food Science, Muthgasse 18, A-1190 Vienna, Austria; University of Zabol, Faculty of Natural Resources, Department of Fisheries, Zabol, Iran
| | - Wolfgang Kneifel
- BOKU - University of Natural Resources and Life Sciences, Department of Food Science and Technology, Institute of Food Science, Muthgasse 18, A-1190 Vienna, Austria
| | - Konrad J Domig
- BOKU - University of Natural Resources and Life Sciences, Department of Food Science and Technology, Institute of Food Science, Muthgasse 18, A-1190 Vienna, Austria
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Sandionigi A, Vicario S, Prosdocimi EM, Galimberti A, Ferri E, Bruno A, Balech B, Mezzasalma V, Casiraghi M. Towards a better understanding of Apis mellifera and Varroa destructor microbiomes: introducing 'phyloh' as a novel phylogenetic diversity analysis tool. Mol Ecol Resour 2014; 15:697-710. [PMID: 25367306 DOI: 10.1111/1755-0998.12341] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 10/23/2014] [Accepted: 10/24/2014] [Indexed: 12/01/2022]
Abstract
The study of diversity in biological communities is an intriguing field. Huge amount of data are nowadays available (provided by the innovative DNA sequencing techniques), and management, analysis and display of results are not trivial. Here, we propose for the first time the use of phylogenetic entropy as a measure of bacterial diversity in studies of microbial community structure. We then compared our new method (i.e. the web tool phyloh) for partitioning phylogenetic diversity with the traditional approach in diversity analyses of bacteria communities. We tested phyloh to characterize microbiome in the honeybee (Apis mellifera, Insecta: Hymenoptera) and its parasitic mite varroa (Varroa destructor, Arachnida: Parasitiformes). The rationale is that the comparative analysis of honeybee and varroa microbiomes could open new perspectives concerning the role of the parasites on honeybee colonies health. Our results showed a dramatic change of the honeybee microbiome when varroa occurs, suggesting that this parasite is able to influence host microbiome. Among the different approaches used, only the entropy method, in conjunction with phylogenetic constraint as implemented in phyloh, was able to discriminate varroa microbiome from that of parasitized honeybees. In conclusion, we foresee that the use of phylogenetic entropy could become a new standard in the analyses of community structure, in particular to prove the contribution of each biological entity to the overall diversity.
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Affiliation(s)
- A Sandionigi
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - S Vicario
- Institute of Biomedical and Technologies (ITB), National Research Council (CNR), Via Giovanni Amendola, 122/D, 70126, Bari, Italy
| | - E M Prosdocimi
- DEFENS, University of Milan, Via Mangiagalli, 25, 20133, Milan, Italy
| | - A Galimberti
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - E Ferri
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - A Bruno
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - B Balech
- Institute of Biomembrane and Bioenergetics (IBBE), National Research Council (CNR), Via Giovanni Amendola, 165/A, 70126, Bari, Italy
| | - V Mezzasalma
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - M Casiraghi
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
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Valliappan K, Sun W, Li Z. Marine actinobacteria associated with marine organisms and their potentials in producing pharmaceutical natural products. Appl Microbiol Biotechnol 2014; 98:7365-77. [PMID: 25064352 DOI: 10.1007/s00253-014-5954-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 07/10/2014] [Accepted: 07/11/2014] [Indexed: 01/09/2023]
Abstract
Actinobacteria are ubiquitous in the marine environment, playing an important ecological role in the recycling of refractory biomaterials and producing novel natural products with pharmic applications. Actinobacteria have been detected or isolated from the marine creatures such as sponges, corals, mollusks, ascidians, seaweeds, and seagrass. Marine organism-associated actinobacterial 16S rRNA gene sequences, i.e., 3,003 sequences, deposited in the NCBI database clearly revealed enormous numbers of actinobacteria associated with marine organisms. For example, RDP classification of these sequences showed that 112 and 62 actinobacterial genera were associated with the sponges and corals, respectively. In most cases, it is expected that these actinobacteria protect the host against pathogens by producing bioactive compounds. Natural products investigation and functional gene screening of the actinobacteria associated with the marine organisms revealed that they can synthesize numerous natural products including polyketides, isoprenoids, phenazines, peptides, indolocarbazoles, sterols, and others. These compounds showed anticancer, antimicrobial, antiparasitic, neurological, antioxidant, and anti-HIV activities. Therefore, marine organism-associated actinobacteria represent an important resource for marine drugs. It is an upcoming field of research to search for novel actinobacteria and pharmaceutical natural products from actinobacteria associated with the marine organisms. In this review, we attempt to summarize the present knowledge on the diversity and natural products production of actinobacteria associated with the marine organisms, based on the publications from 1991 to 2013.
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Affiliation(s)
- Karuppiah Valliappan
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, 200240, Shanghai, China
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Emerging strategies and integrated systems microbiology technologies for biodiscovery of marine bioactive compounds. Mar Drugs 2014; 12:3516-59. [PMID: 24918453 PMCID: PMC4071589 DOI: 10.3390/md12063516] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 12/30/2022] Open
Abstract
Marine microorganisms continue to be a source of structurally and biologically novel compounds with potential use in the biotechnology industry. The unique physiochemical properties of the marine environment (such as pH, pressure, temperature, osmolarity) and uncommon functional groups (such as isonitrile, dichloroimine, isocyanate, and halogenated functional groups) are frequently found in marine metabolites. These facts have resulted in the production of bioactive substances with different properties than those found in terrestrial habitats. In fact, the marine environment contains a relatively untapped reservoir of bioactivity. Recent advances in genomics, metagenomics, proteomics, combinatorial biosynthesis, synthetic biology, screening methods, expression systems, bioinformatics, and the ever increasing availability of sequenced genomes provides us with more opportunities than ever in the discovery of novel bioactive compounds and biocatalysts. The combination of these advanced techniques with traditional techniques, together with the use of dereplication strategies to eliminate known compounds, provides a powerful tool in the discovery of novel marine bioactive compounds. This review outlines and discusses the emerging strategies for the biodiscovery of these bioactive compounds.
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47
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Chiou PP, Chen MJ, Lin CM, Khoo J, Larson J, Holt R, Leong JA, Thorgarrd G, Chen TT. Production of homozygous transgenic rainbow trout with enhanced disease resistance. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:299-308. [PMID: 24085608 PMCID: PMC3996360 DOI: 10.1007/s10126-013-9550-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 09/16/2013] [Indexed: 06/02/2023]
Abstract
Previous studies conducted in our laboratory showed that transgenic medaka expressing cecropin B transgenes exhibited resistant characteristic to fish bacterial pathogens, Pseudomonas fluorescens and Vibrio anguillarum. To confirm whether antimicrobial peptide gene will also exhibit anti-bacterial and anti-viral characteristics in aquaculture important fish species, we produced transgenic rainbow trout expressing cecropin P1 or a synthetic cecropin B analog, CF-17, transgene by sperm-mediated gene transfer method. About 30 % of fish recovered from electroporation were shown to carry the transgene as determined by polymerase chain reaction (PCR) amplification assay. Positive P₁ transgenic fish were crossed to non-transgenic fish to establish F₁ transgenic founder families, and subsequently generating F₂, and F₃ progeny. Expression of cecropin P1 and CF-17 transgenes was detected in transgenic fish by reverse transcription (RT)-PCR analysis. The distribution of body sizes among F₁ transgenic fish were not significantly different from those of non-transgenic fish. Results of challenge studies revealed that many families of F₂ and F₃ transgenic fish exhibited resistance to infection by Aeromonas salmonicida and infectious hematopoietic necrosis virus (IHNV). All-male homozygous cecropin P1 transgenic families were produced by androgenesis from sperm of F₃ heterozygous transgenic fish in one generation. The resistant characteristic to A. salmonicida was confirmed in progeny derived from the outcross of all-male fish to non-transgenic females. Results of our current studies confirmed the possibility of producing disease-resistant homozygous rainbow trout strains by transgenesis of cecropin P1 or CF-17 gene and followed by androgenesis.
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Affiliation(s)
- Pinwen Peter Chiou
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Road, U-3125, Storrs, CT 06269 USA
- Present Address: Marine Research Station, Academia Sinica, Jiaushi, Ilan 262 Taiwan
| | - Maria J. Chen
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Road, U-3125, Storrs, CT 06269 USA
| | - Chun-Mean Lin
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Road, U-3125, Storrs, CT 06269 USA
| | - Jenny Khoo
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Road, U-3125, Storrs, CT 06269 USA
- Present Address: Environmental Protection Authority, Private Bag 63002, Wellington, 6140 New Zealand
| | - Jon Larson
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Road, U-3125, Storrs, CT 06269 USA
| | - Rich Holt
- Department of Microbiology, State University of Oregon, Corvallis, OR 97331 USA
| | - Jo-Ann Leong
- Hawaii Institute of Marine Biology, University of Hawaii, Coconut Island, P.O. Box 1346, Kaneohe, HI 96744 USA
| | - Gary Thorgarrd
- School of Biological Sciences, Washington State University, Pullman, WA 99164 USA
| | - Thomas T. Chen
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Road, U-3125, Storrs, CT 06269 USA
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Yang JY, Sanchez LM, Rath CM, Liu X, Boudreau PD, Bruns N, Glukhov E, Wodtke A, de Felicio R, Fenner A, Ruh Wong W, Linington RG, Zhang L, Debonsi HM, Gerwick WH, Dorrestein PC. Molecular networking as a dereplication strategy. JOURNAL OF NATURAL PRODUCTS 2013; 76:1686-99. [PMID: 24025162 PMCID: PMC3936340 DOI: 10.1021/np400413s] [Citation(s) in RCA: 400] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
A major goal in natural product discovery programs is to rapidly dereplicate known entities from complex biological extracts. We demonstrate here that molecular networking, an approach that organizes MS/MS data based on chemical similarity, is a powerful complement to traditional dereplication strategies. Successful dereplication with molecular networks requires MS/MS spectra of the natural product mixture along with MS/MS spectra of known standards, synthetic compounds, or well-characterized organisms, preferably organized into robust databases. This approach can accommodate different ionization platforms, enabling cross correlations of MS/MS data from ambient ionization, direct infusion, and LC-based methods. Molecular networking not only dereplicates known molecules from complex mixtures, it also captures related analogues, a challenge for many other dereplication strategies. To illustrate its utility as a dereplication tool, we apply mass spectrometry-based molecular networking to a diverse array of marine and terrestrial microbial samples, illustrating the dereplication of 58 molecules including analogues.
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Affiliation(s)
- Jane Y. Yang
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Laura M. Sanchez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Christopher M. Rath
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Xueting Liu
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100190, China
| | - Paul D. Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Nicole Bruns
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Anne Wodtke
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Rafael de Felicio
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Nucleo de Pesquisaem Produtos Naturais e Sinteticos - Departamento de Fisica e Quimica - Faculdade de Ciencias Farmaceuticas de Ribeirao Preto, Universidade de Sao Paulo, Av. Do Café, s/n, Campus Universitario, CEP 14040-903, Ribeirao Preto, Sao Paulo, Brazil
| | - Amanda Fenner
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Weng Ruh Wong
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Roger G. Linington
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Lixin Zhang
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100190, China
| | - Hosana M. Debonsi
- Nucleo de Pesquisaem Produtos Naturais e Sinteticos - Departamento de Fisica e Quimica - Faculdade de Ciencias Farmaceuticas de Ribeirao Preto, Universidade de Sao Paulo, Av. Do Café, s/n, Campus Universitario, CEP 14040-903, Ribeirao Preto, Sao Paulo, Brazil
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Pieter C. Dorrestein
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
- Corresponding Author Telephone: 858-534-6607 Fax: 858-822-0041
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Xing M, Hou Z, Yuan J, Liu Y, Qu Y, Liu B. Taxonomic and functional metagenomic profiling of gastrointestinal tract microbiome of the farmed adult turbot (Scophthalmus maximus). FEMS Microbiol Ecol 2013; 86:432-43. [DOI: 10.1111/1574-6941.12174] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Revised: 06/10/2013] [Accepted: 06/18/2013] [Indexed: 11/27/2022] Open
Affiliation(s)
- Mengxin Xing
- Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
- University of Chinese Academy of Sciences; Beijing China
| | - Zhanhui Hou
- Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
| | - Jianbo Yuan
- Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
- University of Chinese Academy of Sciences; Beijing China
| | - Yuan Liu
- Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
| | - Yanmei Qu
- Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
| | - Bin Liu
- Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
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50
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de Carvalho CCCR, Caramujo MJ. Lipids of prokaryotic origin at the base of marine food webs. Mar Drugs 2012; 10:2698-2714. [PMID: 23342392 PMCID: PMC3528120 DOI: 10.3390/md10122698] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 11/14/2012] [Accepted: 11/22/2012] [Indexed: 11/16/2022] Open
Abstract
In particular niches of the marine environment, such as abyssal trenches, icy waters and hot vents, the base of the food web is composed of bacteria and archaea that have developed strategies to survive and thrive under the most extreme conditions. Some of these organisms are considered "extremophiles" and modulate the fatty acid composition of their phospholipids to maintain the adequate fluidity of the cellular membrane under cold/hot temperatures, elevated pressure, high/low salinity and pH. Bacterial cells are even able to produce polyunsaturated fatty acids, contrarily to what was considered until the 1990s, helping the regulation of the membrane fluidity triggered by temperature and pressure and providing protection from oxidative stress. In marine ecosystems, bacteria may either act as a sink of carbon, contribute to nutrient recycling to photo-autotrophs or bacterial organic matter may be transferred to other trophic links in aquatic food webs. The present work aims to provide a comprehensive review on lipid production in bacteria and archaea and to discuss how their lipids, of both heterotrophic and chemoautotrophic origin, contribute to marine food webs.
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Affiliation(s)
- Carla C. C. R. de Carvalho
- IBB-Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Department of Bioengineering, Instituto Superior Técnico, Technical University of Lisbon, Av. Rovisco Pais, Lisbon 1049-001, Portugal
| | - Maria José Caramujo
- Centre for Environmental Biology, Faculty of Sciences, University of Lisbon, Campo Grande C2, Lisbon 1749-016, Portugal;
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