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Ochoa A, Gastélum G, Rocha J, Olguin LF. High-throughput bacterial co-encapsulation in microfluidic gel beads for discovery of antibiotic-producing strains. Analyst 2023; 148:5762-5774. [PMID: 37843562 DOI: 10.1039/d3an01101a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Bacteria with antagonistic activity inhibit the growth of other bacteria through different mechanisms, including the production of antibiotics. As a result, these microorganisms are a prolific source of such compounds. However, searching for antibiotic-producing strains requires high-throughput techniques due to the vast diversity of microorganisms. Here, we screened and isolated bacteria with antagonistic activity against Escherichia coli expressing the green fluorescent protein (E. coli-GFP). We used microfluidics to co-encapsulate and co-culture single cells from different strains within picoliter gel beads and analyzed them using fluorescence-activated cell sorting (FACS). To test the methodology, we used three bacterial isolates obtained from Mexican maize, which exhibit high, moderate, or no antagonistic activity against E. coli-GFP, as determined previously using agar plate assays. Single cells from each strain were separately co-incubated into gel beads with E. coli-GFP. We monitored the development of the maize bacteria microcolonies and tracked the growth or inhibition of E. coli-GFP using bright-field and fluorescent microscopy. We correlated these images with distinctive light scatter and fluorescence signatures of each incubated bead type using FACS. This analysis enabled us to sort gel beads filled with an antagonistic strain, starting from a mixture of the three different types of maize bacteria and E. coli-GFP. Likewise, culturing the FACS-sorted beads on agar plates confirmed the isolation and recovery of the two antagonistic strains. In addition, enrichment assays demonstrated the methodology's effectiveness in isolating rare antibiotic-producer strains (0.01% abundance) present in a mixture of microorganisms. These results show that associating light side scatter and fluorescent flow cytometry signals with microscopy images provides valuable controls to establish successful high-throughput methods for sorting beads in which microbial interaction assays are performed.
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Affiliation(s)
- Abraham Ochoa
- Laboratorio de Biofisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Coyoacán, CDMX 04510, Mexico.
| | - Gabriela Gastélum
- Unidad Regional Hidalgo, Centro de Investigación en Alimentación y Desarrollo A.C., San Agustín Tlaxiaca, Hidalgo 42163, Mexico
| | - Jorge Rocha
- Unidad Regional Hidalgo, Centro de Investigación en Alimentación y Desarrollo A.C., San Agustín Tlaxiaca, Hidalgo 42163, Mexico
- Programa de Agricultura en Zonas Áridas, Centro de Investigaciones Biológicas del Noroeste, La Paz, B.C.S. 23096, Mexico
| | - Luis F Olguin
- Laboratorio de Biofisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Coyoacán, CDMX 04510, Mexico.
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Baranova AA, Alferova VA, Korshun VA, Tyurin AP. Modern Trends in Natural Antibiotic Discovery. Life (Basel) 2023; 13:life13051073. [PMID: 37240718 DOI: 10.3390/life13051073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/10/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Natural scaffolds remain an important basis for drug development. Therefore, approaches to natural bioactive compound discovery attract significant attention. In this account, we summarize modern and emerging trends in the screening and identification of natural antibiotics. The methods are divided into three large groups: approaches based on microbiology, chemistry, and molecular biology. The scientific potential of the methods is illustrated with the most prominent and recent results.
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Affiliation(s)
- Anna A Baranova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, 119021 Moscow, Russia
| | - Vera A Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, 119021 Moscow, Russia
| | - Vladimir A Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Anton P Tyurin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
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Shmygarev VI, Prokopenko Y, Terekhov SS, Zakharova MY, Dubinnyi MA, Smirnov IV, Yampolsky IV, Tsarkova AS. Amicoumacin-based prodrug development approach. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2022. [DOI: 10.24075/brsmu.2022.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Coronavirus disease COVID-19, caused by the SARS-CoV-2 virus, is highly contagious and has a severe morbidity. Providing care to patients with COVID-19 requires the development of new types of antiviral drugs. The aim of this work is to develop a prodrug for the treatment of coronavirus disease using the antibiotic Amicoumacin A (Ami), the mechanism of action of which is based on translation inhibition. Enzymatic hydrolysis of an inactivated prodrug by the SARS-CoV-2 main protease can lead to the release of the active Ami molecule and, as a consequence, the suppression of protein biosynthesis in infected cells. To test the proposed hypothesis, a five-stage synthesis of an inactivated analogue of Amicoumacin A was carried out. Its in vitro testing with the SARS-CoV-2 recombinant protease MPro showed a low percentage of hydrolysis. Further optimization of the peptide fragment of the inactivated analog recognized by the SARS-CoV-2 MPro protease may lead to an increase in proteolysis and the release of Amicoumacin A.
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Affiliation(s)
- VI Shmygarev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - YuA Prokopenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - SS Terekhov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - MYu Zakharova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - MA Dubinnyi
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - IV Smirnov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - IV Yampolsky
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia;Pirogov Russian National Research Medical University, Moscow, Russia
| | - AS Tsarkova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
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Baranova MN, Kudzhaev AM, Mokrushina YA, Babenko VV, Kornienko MA, Malakhova MV, Yudin VG, Rubtsova MP, Zalevsky A, Belozerova OA, Kovalchuk S, Zhuravlev YN, Ilina EN, Gabibov AG, Smirnov IV, Terekhov SS. Deep Functional Profiling of Wild Animal Microbiomes Reveals Probiotic Bacillus pumilus Strains with a Common Biosynthetic Fingerprint. Int J Mol Sci 2022; 23:ijms23031168. [PMID: 35163108 PMCID: PMC8835302 DOI: 10.3390/ijms23031168] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/07/2022] [Accepted: 01/17/2022] [Indexed: 02/06/2023] Open
Abstract
The biodiversity of microorganisms is maintained by intricate nets of interactions between competing species. Impaired functionality of human microbiomes correlates with their reduced biodiversity originating from aseptic environmental conditions and antibiotic use. Microbiomes of wild animals are free of these selective pressures. Microbiota provides a protecting shield from invasion by pathogens in the wild, outcompeting their growth in specific ecological niches. We applied ultrahigh-throughput microfluidic technologies for functional profiling of microbiomes of wild animals, including the skin beetle, Siberian lynx, common raccoon dog, and East Siberian brown bear. Single-cell screening of the most efficient killers of the common human pathogen Staphylococcus aureus resulted in repeated isolation of Bacillus pumilus strains. While isolated strains had different phenotypes, all of them displayed a similar set of biosynthetic gene clusters (BGCs) encoding antibiotic amicoumacin, siderophore bacillibactin, and putative analogs of antimicrobials including bacilysin, surfactin, desferrioxamine, and class IId cyclical bacteriocin. Amicoumacin A (Ami) was identified as a major antibacterial metabolite of these strains mediating their antagonistic activity. Genome mining indicates that Ami BGCs with this architecture subdivide into three distinct families, characteristic of the B. pumilus, B. subtilis, and Paenibacillus species. While Ami itself displays mediocre activity against the majority of Gram-negative bacteria, isolated B. pumilus strains efficiently inhibit the growth of both Gram-positive S. aureus and Gram-negative E. coli in coculture. We believe that the expanded antagonistic activity spectrum of Ami-producing B. pumilus can be attributed to the metabolomic profile predetermined by their biosynthetic fingerprint. Ultrahigh-throughput isolation of natural probiotic strains from wild animal microbiomes, as well as their metabolic reprogramming, opens up a new avenue for pathogen control and microbiome remodeling in the food industry, agriculture, and healthcare.
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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.M.K.); (Y.A.M.); (A.Z.); (O.A.B.); (S.K.)
| | - Arsen M. Kudzhaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.M.K.); (Y.A.M.); (A.Z.); (O.A.B.); (S.K.)
| | - Yuliana A. Mokrushina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.M.K.); (Y.A.M.); (A.Z.); (O.A.B.); (S.K.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Vladislav V. Babenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (V.V.B.); (M.A.K.); (M.V.M.); (E.N.I.)
| | - Maria A. Kornienko
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (V.V.B.); (M.A.K.); (M.V.M.); (E.N.I.)
| | - Maja V. Malakhova
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (V.V.B.); (M.A.K.); (M.V.M.); (E.N.I.)
| | - Victor G. Yudin
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, 690022 Vladivostok, Russia; (V.G.Y.); (Y.N.Z.)
| | - Maria P. Rubtsova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Arthur Zalevsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.M.K.); (Y.A.M.); (A.Z.); (O.A.B.); (S.K.)
| | - Olga A. Belozerova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.M.K.); (Y.A.M.); (A.Z.); (O.A.B.); (S.K.)
| | - Sergey Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.M.K.); (Y.A.M.); (A.Z.); (O.A.B.); (S.K.)
| | - Yuriy N. Zhuravlev
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, 690022 Vladivostok, Russia; (V.G.Y.); (Y.N.Z.)
| | - Elena N. Ilina
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (V.V.B.); (M.A.K.); (M.V.M.); (E.N.I.)
| | - Alexander G. Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.M.K.); (Y.A.M.); (A.Z.); (O.A.B.); (S.K.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Correspondence: (A.G.G.); (I.V.S.); (S.S.T.)
| | - Ivan V. Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.M.K.); (Y.A.M.); (A.Z.); (O.A.B.); (S.K.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Correspondence: (A.G.G.); (I.V.S.); (S.S.T.)
| | - Stanislav S. Terekhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.M.K.); (Y.A.M.); (A.Z.); (O.A.B.); (S.K.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Correspondence: (A.G.G.); (I.V.S.); (S.S.T.)
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5
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Uzoukwu EU, Phandanouvong-Lozano V, Usman H, Sfeir C, Niepa THR. Droplet-based microsystems as novel assessment tools for oral microbial dynamics. Biotechnol Adv 2022; 55:107903. [PMID: 34990774 DOI: 10.1016/j.biotechadv.2021.107903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 12/03/2021] [Accepted: 12/30/2021] [Indexed: 12/11/2022]
Abstract
The human microbiome comprises thousands of microbial species that live in and on the body and play critical roles in human health and disease. Recent findings on the interplay among members of the oral microbiome, defined by a personalized set of microorganisms, have elucidated the role of bacteria and yeasts in oral health and diseases including dental caries, halitosis, and periodontal infections. However, the majority of these studies rely on traditional culturing methods which are limited in their ability of replicating the oral microenvironment, and therefore fail to evaluate key microbial interactions in microbiome dynamics. Novel culturing methods have emerged to address this shortcoming. Here, we reviewed the potential of droplet-based microfluidics as an alternative approach for culturing microorganisms and assessing the oral microbiome dynamics. We discussed the state of the art and recent progress in the field of oral microbiology. Although at its infancy, droplet-based microtechnology presents an interesting potential for elucidating oral microbial dynamics and pathophysiology. We highlight how new findings provided by current microfluidic-based methodologies could advance the investigation of the oral microbiome. We anticipate that our work involving the droplet-based microfluidic technique with a semipermeable membrane will lay the foundations for future microbial dynamics studies and further expand the knowledge of the oral microbiome and its implication in oral health.
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Affiliation(s)
| | | | - Huda Usman
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, PA, USA
| | - Charles Sfeir
- Department of Bioengineering, University of Pittsburgh, PA, USA; Department of Periodontics and Preventive Dentistry, University of Pittsburgh, PA, USA; Department of Oral Biology, University of Pittsburgh, PA, USA; The Center for Craniofacial Regeneration, University of Pittsburgh, PA, USA; The McGowan Institute for Regenerative Medicine, University of Pittsburgh, PA, USA
| | - Tagbo H R Niepa
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, PA, USA; Department of Bioengineering, University of Pittsburgh, PA, USA; Department of Civil and Environmental Engineering, University of Pittsburgh, PA, USA; Department of Mechanical Engineering and Materials Science, University of Pittsburgh, PA, USA; Center for Medicine and the Microbiome, University of Pittsburgh, PA, USA; The McGowan Institute for Regenerative Medicine, University of Pittsburgh, PA, USA.
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6
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Baranova MN, Babikova PA, Kudzhaev AM, Mokrushina YA, Belozerova OA, Yunin MA, Kovalchuk S, Gabibov AG, Smirnov IV, Terekhov SS. Live Biosensors for Ultrahigh-Throughput Screening of Antimicrobial Activity against Gram-Negative Bacteria. Antibiotics (Basel) 2021; 10:antibiotics10101161. [PMID: 34680742 PMCID: PMC8532632 DOI: 10.3390/antibiotics10101161] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 12/29/2022] Open
Abstract
Gram-negative pathogens represent an urgent threat due to their intrinsic and acquired antibiotic resistance. Many recent drug candidates display prominent antimicrobial activity against Gram-positive bacteria being inefficient against Gram-negative pathogens. Ultrahigh-throughput, microfluidics-based screening techniques represent a new paradigm for deep profiling of antibacterial activity and antibiotic discovery. A key stage of this technology is based on single-cell cocultivation of microbiome biodiversity together with reporter fluorescent pathogen in emulsion, followed by the selection of reporter-free droplets using fluorescence-activated cell sorting. Here, a panel of reporter strains of Gram-negative bacteria Escherichia coli was developed to provide live biosensors for precise monitoring of antimicrobial activity. We optimized cell morphology, fluorescent protein, and selected the most efficient promoters for stable, homogeneous, high-level production of green fluorescent protein (GFP) in E. coli. Two alternative strategies based on highly efficient constitutive promoter pJ23119 or T7 promoter leakage enabled sensitive fluorescent detection of bacterial growth and killing. The developed live biosensors were applied for isolating potent E. coli-killing Paenibacillus polymyxa P4 strain by the ultrahigh-throughput screening of soil microbiome. The multi-omics approach revealed antibiotic colistin (polymyxin E) and its biosynthetic gene cluster, mediating antibiotic activity. Live biosensors may be efficiently implemented for antibiotic/probiotic discovery, environmental monitoring, and synthetic biology.
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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.); (P.A.B.); (A.M.K.); (Y.A.M.); (O.A.B.); (M.A.Y.); (S.K.)
| | - Polina A. Babikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (P.A.B.); (A.M.K.); (Y.A.M.); (O.A.B.); (M.A.Y.); (S.K.)
| | - Arsen M. Kudzhaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (P.A.B.); (A.M.K.); (Y.A.M.); (O.A.B.); (M.A.Y.); (S.K.)
| | - Yuliana A. Mokrushina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (P.A.B.); (A.M.K.); (Y.A.M.); (O.A.B.); (M.A.Y.); (S.K.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Olga A. Belozerova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (P.A.B.); (A.M.K.); (Y.A.M.); (O.A.B.); (M.A.Y.); (S.K.)
| | - Maxim A. Yunin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (P.A.B.); (A.M.K.); (Y.A.M.); (O.A.B.); (M.A.Y.); (S.K.)
| | - Sergey Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (P.A.B.); (A.M.K.); (Y.A.M.); (O.A.B.); (M.A.Y.); (S.K.)
| | - Alexander G. Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (P.A.B.); (A.M.K.); (Y.A.M.); (O.A.B.); (M.A.Y.); (S.K.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: (A.G.G.); (I.V.S.); (S.S.T.)
| | - Ivan V. Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (P.A.B.); (A.M.K.); (Y.A.M.); (O.A.B.); (M.A.Y.); (S.K.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: (A.G.G.); (I.V.S.); (S.S.T.)
| | - Stanislav S. Terekhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (P.A.B.); (A.M.K.); (Y.A.M.); (O.A.B.); (M.A.Y.); (S.K.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: (A.G.G.); (I.V.S.); (S.S.T.)
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7
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A new, reliable, and high-throughput strategy to screen bacteria for antagonistic activity against Staphylococcus aureus. BMC Microbiol 2021; 21:189. [PMID: 34167492 PMCID: PMC8228506 DOI: 10.1186/s12866-021-02265-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/10/2021] [Indexed: 01/20/2023] Open
Abstract
Background Antibiotic-resistant Staphylococcus aureus clones have emerged globally over the last few decades. Probiotics have been actively studied as an alternative to antibiotics to prevent and treat S. aureus infections, but identifying new probiotic bacteria, that have antagonistic activity against S. aureus, is difficult since traditional screening strategies are time-consuming and expensive. Here, we describe a new plasmid-based method which uses highly stable plasmids to screen bacteria with antagonistic activity against S. aureus. Results We have created two recombinant plasmids (pQS1 and pQS3) which carry either gfpbk or mCherry under the control of a S. aureus quorum-sensing (QS) promoter (agrP3). Using this recombinant plasmid pair, we tested 81 bacteria isolated from Holstein dairy milk to identify bacteria that had growth-inhibiting activity against S. aureus and suggest potential explanations for the growth inhibition. The stability test illustrated that pQS1 and pQS3 remained highly stable for at least 24 h in batch culture conditions without selection pressure from antibiotics. This allowed co-culturing of S. aureus with other bacteria. Using the newly developed pQS plasmids, we found commensal bacteria, isolated from raw bovine milk, which had growth-inhibiting activity (n = 13) and quorum-quenching (QQ) activity (n = 13) towards both S. aureus Sa25 (CC97) and Sa27 (CC151). The pQS-based method is efficient and effective for simultaneously screening growth-inhibiting and QQ bacteria against S. aureus on agar media. Conclusions It was shown that growth-inhibiting and QQ activity toward pQS plasmid transformants of S. aureus can be simultaneously monitored by observing the zone of growth inhibition and reporter protein inhibition on agar plates. Newly identified antagonistic bacteria and their functional biomolecules are promising candidates for future development of probiotic drugs and prophylactics/therapeutics for bacterial infections including S. aureus. Furthermore, this new approach can be a useful method to find bacteria that can be used to prevent and treat S. aureus infections in both humans and animals. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02265-4.
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Shablykina OV, Shilin SV, Moskvina VS, Ishchenko VV, Khilya VP. Progress in the Chemistry of Amino-Acid Derivatives of Isocoumarins and 3,4-Dihydroisocoumarins. Chem Nat Compd 2021. [DOI: 10.1007/s10600-021-03323-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Yang J, Zhu Q, Xu F, Yang M, Du H, Bian X, Lu Z, Lu Y, Lu F. Genome Mining, Heterologous Expression, Antibacterial and Antioxidant Activities of Lipoamides and Amicoumacins from Compost-Associated Bacillus subtilis fmb60. Molecules 2021; 26:molecules26071892. [PMID: 33810551 PMCID: PMC8036425 DOI: 10.3390/molecules26071892] [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: 03/02/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 11/25/2022] Open
Abstract
Bacillus subtilis fmb60, which has broad-spectrum antimicrobial activities, was isolated from plant straw compost. A hybrid NRPS/PKS cluster was screened from the genome. Sixteen secondary metabolites produced by the gene cluster were isolated and identified using LC-HRMS and NMR. Three lipoamides D–F (1–3) and two amicoumacin derivatives, amicoumacins D, E (4, 5), were identified, and are reported here for the first time. Lipoamides D–F exhibited strong antibacterial activities against harmful foodborne bacteria, with the MIC ranging from 6.25 to 25 µg/mL. Amicoumacin E scavenged 38.8% of ABTS+ radicals at 1 mg/mL. Direct cloning and heterologous expression of the NRPS/PKS and ace gene cluster identified its importance for the biosynthesis of amicoumacins. This study demonstrated that there is a high potential for biocontrol utilization of B. subtilis fmb60, and genome mining for clusters of secondary metabolites of B. subtilis fmb60 has revealed a greater biosynthetic potential for the production of novel natural products than previously anticipated.
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Affiliation(s)
- Jie Yang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; (J.Y.); (Q.Z.); (F.X.)
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- Jiangsu Marine Resources Development Research Institute, Lianyungang 222000, China
| | - Qingzheng Zhu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; (J.Y.); (Q.Z.); (F.X.)
| | - Feng Xu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; (J.Y.); (Q.Z.); (F.X.)
| | - Ming Yang
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (M.Y.); (X.B.)
| | - Hechao Du
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China; (H.D.); (Z.L.)
| | - Xiaoying Bian
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (M.Y.); (X.B.)
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China; (H.D.); (Z.L.)
| | - Yingjian Lu
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210003, China
- Correspondence: (Y.L.); (F.L.); Tel./Fax: +86-258-439-5155 (Y.L.); +86-258-439-5963 (F.L.)
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China; (H.D.); (Z.L.)
- Correspondence: (Y.L.); (F.L.); Tel./Fax: +86-258-439-5155 (Y.L.); +86-258-439-5963 (F.L.)
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Wang D, Li J, Zhu G, Zhao K, Jiang W, Li H, Wang W, Kumar V, Dong S, Zhu W, Tian X. Mechanism of the Potential Therapeutic Candidate Bacillus subtilis BSXE-1601 Against Shrimp Pathogenic Vibrios and Multifunctional Metabolites Biosynthetic Capability of the Strain as Predicted by Genome Analysis. Front Microbiol 2020; 11:581802. [PMID: 33193216 PMCID: PMC7649127 DOI: 10.3389/fmicb.2020.581802] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/30/2020] [Indexed: 12/02/2022] Open
Abstract
The global shrimp industry has suffered bacterial diseases caused mainly by Vibrio species. The typical vibriosis, acute hepatopancreatic necrosis disease (AHPND), has resulted in mass mortality and devastating economic losses. Thus, therapeutic strategies are highly needed to decrease the risk of vibriosis outbreaks. Herein, we initially identified that the growth of the causative agent of AHPND, Vibrio parahaemolyticus (VP AHPND ) and other vibrios in Pacific white shrimp (Litopenaeus vannamei) was inhibited by a Bacillus subtilis strain BSXE-1601. The natural products amicoumacins A, B, and C were purified from the cell-free supernatant from the strain BSXE-1601, but only amicoumacin A was demonstrated to be responsible for this anti-Vibrio activity. Our discovery provided the first evidence that amicoumacin A was highly active against shrimp pathogens, including the representative strain VP AHPND . Furthermore, we elucidated the amicoumacin A biosynthetic gene cluster by whole genome sequencing of the B. subtilis strain BSXE-1601. In addition to amicoumacin A, the strain BSXE-1601 genome harbored other genes encoding bacillibactin, fengycin, surfactin, bacilysin, and subtilosin A, all of which have previously reported antagonistic activities against pathogenic strains. The whole-genome analysis provided unequivocal evidence in support of the huge potential of the strain BSXE-1601 to produce diverse biologically antagonistic natural products, which may facilitate further studies on the effective therapeutics for detrimental diseases in shrimp.
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Affiliation(s)
- Dongdong Wang
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
- Lab of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jiahui Li
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Guoliang Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Kun Zhao
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Wenwen Jiang
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Haidong Li
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Wenjun Wang
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Vikash Kumar
- Lab of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Shuanglin Dong
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Weiming Zhu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiangli Tian
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
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Abstract
DNA libraries are predisposed to template mispairing during conventional “bulk” PCR, leading to the loss of unique sequences. The latter is facilitated by the nonuniform distribution of templates frequently observed in DNA libraries. These effects result in a prominent reduction of the original diversity. The encapsulation of DNA repertoires in liquid droplets abolishes the effects of mispairing in DNA libraries. The fundamental advantages of emulsion PCR (ePCR) over bulk PCR are illustrated by deep sequencing and mathematical modeling, which provide the general strategy for ePCR rationalization. The quasi single-molecule ePCR reveals total genetic information by counteracting the degeneration of DNA libraries’ diversity. Conventional “bulk” PCR often yields inefficient and nonuniform amplification of complex templates in DNA libraries, introducing unwanted biases. Amplification of single DNA molecules encapsulated in a myriad of emulsion droplets (emulsion PCR, ePCR) allows the mitigation of this problem. Different ePCR regimes were experimentally analyzed to identify the most robust techniques for enhanced amplification of DNA libraries. A phenomenological mathematical model that forms an essential basis for optimal use of ePCR for library amplification was developed. A detailed description by high-throughput sequencing of amplified DNA-encoded libraries highlights the principal advantages of ePCR over bulk PCR. ePCR outperforms PCR, reduces gross DNA errors, and provides a more uniform distribution of the amplified sequences. The quasi single-molecule amplification achieved via ePCR represents the fundamental requirement in case of complex DNA templates being prone to diversity degeneration and provides a way to preserve the quality of DNA libraries.
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Selective Eradication of Staphylococcus aureus by the Designer Genetically Programmed Yeast Biocontrol Agent. Antibiotics (Basel) 2020; 9:antibiotics9090527. [PMID: 32824911 PMCID: PMC7559405 DOI: 10.3390/antibiotics9090527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/07/2020] [Accepted: 08/18/2020] [Indexed: 12/29/2022] Open
Abstract
Staphylococcus aureus is a common human pathogen that is particularly often associated with antibiotic resistance. The eradication of this ubiquitous infectious agent from its ecological niches and contaminated surfaces is especially complicated by excessive biofilm formation and persisting cells, which evade the antibacterial activity of conventional antibiotics. Here, we present an alternative view of the problem of specific S. aureus eradication. The constitutive heterologous production of highly specific bacteriolytic protease lysostaphin in yeast Pichia pastoris provides an efficient biocontrol agent, specifically killing S. aureus in coculture. A yeast-based anti-S. aureus probiotic was efficient in a high range of temperatures and target-to-effector ratios, indicating its robustness and versatility in eliminating S. aureus cells. The efficient eradication of S. aureus by live lysostaphin-producing P. pastoris was achieved at high scales, providing a simple, biocompatible and cost-effective strategy for S. aureus lysis in bioproduction and surface decontamination. Future biomedical applications based on designer yeast biocontrol agents require evaluation in in vivo models. However, we believe that this strategy is very promising since it provides highly safe, efficient and selective genetically programmed probiotics and targeted biocontrol agents.
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New Insights into Antibacterial Compounds: From Synthesis and Discovery to Molecular Mechanisms of Action. Antibiotics (Basel) 2020; 9:antibiotics9080471. [PMID: 32752219 PMCID: PMC7459480 DOI: 10.3390/antibiotics9080471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 12/24/2022] Open
Abstract
The worldwide emergence of microbial resistance to available antibiotics presents a global threat to public health and health systems. This special issue aimed to gather papers describing novel antibiotics, originating form chemical synthesis, repurposing of existent drugs, or from natural sources like plant extracts, herbs and spices. A total of 13 papers were published, covering a wide range of topic, including antimicrobial resistance surveillance studies; synthesis of novel molecules with antimicrobial activities; modification or repurposing of already existing molecules, plant-derived active extracts, and molecules; the effects of antimicrobial therapy on microbiota; and the investigation of novel formulations for human and veterinary uses. After decades of antibiotics discovery decline, antibiotics discovery is boosting. Recent developments of post genomics approaches and bioinformatics tools will most certainly turn the tide in the discovery and development of antimicrobials in this exciting field.
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