151
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Qiu H, Shen F, Yin A, Liu J, Wu B, Li Y, Xiao Y, Hai J, Xu B. Biodegradation and Detoxification of Azo Dyes by Halophilic/Halotolerant Microflora Isolated From the Salt Fields of Tibet Autonomous Region China. Front Microbiol 2022; 13:877151. [PMID: 35620106 PMCID: PMC9127808 DOI: 10.3389/fmicb.2022.877151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/11/2022] [Indexed: 12/03/2022] Open
Abstract
This study aimed to decolorize azo dyes in high-salt industrial wastewater under high-salt and low oxygen conditions using extreme halophilic/halotolerant bacteria screened from the salt fields of Tibet, which consisted of Enterococcus, unclassified Enterobacteriaceae, Staphylococcus, Bacillus, and Kosakonia. Under the optimal conditions, 600 mg/l Congo red, Direct Black G (DBG), Amaranth, methyl red, and methyl orange could be completely decolorized in 24, 8, 8, 12, and 12 h, respectively. When the DBG concentration was 600 mg/l, NADH–DCIP, laccase, and azo reductase were confirmed to be the primary reductase and oxidase during the degradation process, and the degradation pathways were verified. The microflora could not only tolerate changes in salt concentrations of 0–80 g/l, but also displayed strong degradative ability. Under high-salt concentrations (≥ 60 g/l NaCl), NADH–DCIP reductase was primarily used to decolorize the azo dye. However, under low salt concentrations (≤ 40 g/l NaCl), azo reductase began to function, and manganese peroxidase and lignin peroxidase could cooperate to participate in DBG degradation. Additionally, the halophilic/halophilic microflora was shown to convert the toxic DBG dye to metabolites of low toxicity based on phytotoxicity analysis, and a new mechanism for the microflora to degrade DBG was proposed based on intermediates identified by liquid chromatography-mass spectrometry (LC–MS). This study revealed that the halophilic/halophilic microflora has effective ecological and industrial value for treating wastewater from the textile industry.
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Affiliation(s)
- Hulin Qiu
- College of Biological and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, China
| | - Fengfei Shen
- College of Biological and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, China
| | - Aiguo Yin
- College of Biological and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
| | - Jiaxian Liu
- College of Biological and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, China
| | - Biyu Wu
- College of Biological and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, China
| | - Ying Li
- College of Biological and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, China
| | - Yunyi Xiao
- College of Biological and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, China
| | - Jinping Hai
- College of Biological and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, China
| | - Bo Xu
- College of Biological and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
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152
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Iquebal MA, Jagannadham J, Jaiswal S, Prabha R, Rai A, Kumar D. Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review. Front Microbiol 2022; 13:708335. [PMID: 35655999 PMCID: PMC9152772 DOI: 10.3389/fmicb.2022.708335] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 03/17/2022] [Indexed: 12/12/2022] Open
Abstract
Agricultural productivity is highly influenced by its associated microbial community. With advancements in omics technology, metagenomics is known to play a vital role in microbial world studies by unlocking the uncultured microbial populations present in the environment. Metagenomics is a diagnostic tool to target unique signature loci of plant and animal pathogens as well as beneficial microorganisms from samples. Here, we reviewed various aspects of metagenomics from experimental methods to techniques used for sequencing, as well as diversified computational resources, including databases and software tools. Exhaustive focus and study are conducted on the application of metagenomics in agriculture, deciphering various areas, including pathogen and plant disease identification, disease resistance breeding, plant pest control, weed management, abiotic stress management, post-harvest management, discoveries in agriculture, source of novel molecules/compounds, biosurfactants and natural product, identification of biosynthetic molecules, use in genetically modified crops, and antibiotic-resistant genes. Metagenomics-wide association studies study in agriculture on crop productivity rates, intercropping analysis, and agronomic field is analyzed. This article is the first of its comprehensive study and prospects from an agriculture perspective, focusing on a wider range of applications of metagenomics and its association studies.
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Affiliation(s)
- Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Jaisri Jagannadham
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ratna Prabha
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
- School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
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153
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Fernández-Fernández R, Lozano C, Eguizábal P, Ruiz-Ripa L, Martínez-Álvarez S, Abdullahi IN, Zarazaga M, Torres C. Bacteriocin-Like Inhibitory Substances in Staphylococci of Different Origins and Species With Activity Against Relevant Pathogens. Front Microbiol 2022; 13:870510. [PMID: 35558130 PMCID: PMC9087342 DOI: 10.3389/fmicb.2022.870510] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/15/2022] [Indexed: 12/31/2022] Open
Abstract
Bacteriocins are antimicrobial peptides with relevance in the modulation of human and animal microbiota that have gained interest in biomedical and biotechnological applications. In this study, the production of bacteriocin-like inhibitory substances (BLIS) was tested among a collection of 890 staphylococci of different origins (humans, animals, food, and the environment) and species, both coagulase-positive (CoPS, 238 isolates of 3 species) and coagulase-negative staphylococci (CoNS, 652 isolates of 26 species). Of the 890 staphylococci, 60 (6.7%) showed antimicrobial activity by the spot-on-lawn method against at least one of the 25 indicator bacteria tested. BLIS-producer (BLIS+) isolates were detected in 8.8% of CoPS and 6.0% of CoNS. The staphylococcal species with the highest percentages of BLIS+ isolates were S. chromogenes (38.5%), S. pseudintermedius (26.7%), and S. warneri (23.1%). The production of BLIS was more frequently detected among isolates of pets, wild animals, and food. Moreover, 13 BLIS+ isolates showed wide antimicrobial activiy spectrum, and 7 of these isolates (of species S. aureus, S. pseudintermedius, S. sciuri, and S. hominis) demonstrated antimicrobial activity against more than 70% of the indicator bacteria tested. The genetic characterization (by PCR and sequencing) of the 60 BLIS+ isolates revealed the detection of (a) 11 CoNS and CoPS isolates carrying putative lantibiotic-like genes; (b) 3 S. pseudintermedius isolates harboring the genes of BacSp222 bacteriocin; and (c) 2 S. chromogenes isolates that presented the gene of a putative cyclic bacteriocin (uberolysin-like), being the first report in this CoNS species. Antimicrobial susceptibility testing was performed in BLIS+ isolates and one-third of the CoNS isolates showed susceptibility to all antibiotics tested, which also lacked the virulence genes studied. These BLIS+ CoNS are good candidates for further characterization studies.
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Affiliation(s)
- Rosa Fernández-Fernández
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Carmen Lozano
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Paula Eguizábal
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Laura Ruiz-Ripa
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Sandra Martínez-Álvarez
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Idris Nasir Abdullahi
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
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154
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Chu CY. Targeting the cutaneous microbiota in atopic dermatitis: 'A new hope' or 'attack of the CoNS'? Clin Transl Med 2022; 12:e865. [PMID: 35542966 PMCID: PMC9091992 DOI: 10.1002/ctm2.865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 12/02/2022] Open
Abstract
Although evidence showing that Staphylococcus aureus (S. aureus) is directly causative of atopic dermatitis (AD) is still lacking, there is evidence that S. aureus abundance is associated with disease flares and therapeutic responses. Patients receiving ATx201 OINTMENT 2% twice‐daily had a significant reduction in the abundance of S. aureus and increasing Shannon diversity of skin microbiome compared to vehicle after seven days. A small molecule with a narrow‐spectrum effect, especially on S. aureus, might be an attractive alternative for the treatment of AD.
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Affiliation(s)
- Chia-Yu Chu
- Department of Dermatology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
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155
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Ma K, Chen W, Yan SQ, Liu ZZ, Lin XQ, Zhang JB, Gao Y, Wang T, Zhang JG, Yang YJ. Purification, Characterization, Mode of Action, and Application of Jileicin, a Novel Antimicrobial from Paenibacillus jilinensis YPG26. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:5570-5578. [PMID: 35499918 PMCID: PMC9104118 DOI: 10.1021/acs.jafc.2c01458] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Antimicrobial compounds from the commensal gut microbiota have gained much attention due to their multifunctionality in maintaining good health in the host and killing multidrug-resistant bacteria. Our previous study showed that Paenibacillus jilinensis YPG26 isolated from chicken intestine can antagonize multiple pathogens. Herein, we characterized a bacteriocin-like inhibitory substance, jileicin, purified from P. jilinensis YPG26. Mass spectrometry analysis revealed that jileicin was a protein consisting of 211 amino acids, which showed 88.98% identity to the SIMPL domain-containing protein. The jileicin showed a relatively broad-spectrum antibacterial ability, especially against enterococci. Additionally, the jileicin exhibited good stability after various treatments, no detectable resistance, no significant cytotoxicity, and very low levels of hemolytic activity. The mode of action against Enterococcus faecium demonstrated that jileicin could destroy cell membrane integrity, increase cell membrane permeability, and eventually lead to cell death. Furthermore, jileicin was efficient in controlling the growth of E. faecium in milk. In conclusion, jileicin, as a newly identified antibacterial agent, is expected to be a promising candidate for application in the food, pharmaceutical, and biomedical industries.
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156
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Role of Antimicrobial Drug in the Development of Potential Therapeutics. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:2500613. [PMID: 35571735 PMCID: PMC9098294 DOI: 10.1155/2022/2500613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 12/17/2022]
Abstract
Population of the world run into several health-related emergencies among mankind and humans as it creates a challenge for the evolution of novel drug discoveries. One such can be the emergence of multidrug-resistant (MDR) strains in both hospital and community settings, which have been due to an inappropriate use and inadequate control of antibiotics that has led to the foremost human health concerns with a high impact on the global economy. So far, there has been application of two strategies for the development of anti-infective agents either by classical antibiotics that have been derived for their synthetic analogs with increased efficacy or screening natural compounds along with the synthetic compound libraries for the antimicrobial activities. However, need for newer treatment options for infectious diseases has led research to develop new generation of antimicrobial activity to further lessen the spread of antibiotic resistance. Currently, the principles aim to find novel mode of actions or products to target the specific sites and virulence factors in pathogens by a series of better understanding of physiology and molecular aspects of the microbial resistance, mechanism of infection process, and gene-pathogenicity relationship. The design various novel strategies tends to provide us a path for the development of various antimicrobial therapies that intends to have a broader and wider antimicrobial spectrum that helps to combat MDR strains worldwide. The development of antimicrobial peptides, metabolites derived from plants, microbes, phage-based antimicrobial agents, use of metal nanoparticles, and role of CRISPR have led to an exceptional strategies in designing and developing the next-generation antimicrobials. These novel strategies might help to combat the seriousness of the infection rates and control the health crisis system.
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157
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In vivo growth of Staphylococcus lugdunensis is facilitated by the concerted function of heme and non-heme iron acquisition mechanisms. J Biol Chem 2022; 298:101823. [PMID: 35283192 PMCID: PMC9052147 DOI: 10.1016/j.jbc.2022.101823] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 12/23/2022] Open
Abstract
Staphylococcus lugdunensis has increasingly been recognized as a pathogen that can cause serious infection indicating this bacterium overcomes host nutritional immunity. Despite this, there exists a significant knowledge gap regarding the iron acquisition mechanisms employed by S. lugdunensis, especially during infection of the mammalian host. Here we show that S. lugdunensis can usurp hydroxamate siderophores and staphyloferrin A and B from Staphylococcus aureus. These transport activities all required a functional FhuC ATPase. Moreover, we show that the acquisition of catechol siderophores and catecholamine stress hormones by S. lugdunensis required the presence of the sst-1 transporter-encoding locus, but not the sst-2 locus. Iron-dependent growth in acidic culture conditions necessitated the ferrous iron transport system encoded by feoAB. Heme iron was acquired via expression of the iron-regulated surface determinant (isd) locus. During systemic infection of mice, we demonstrated that while S. lugdunensis does not cause overt illness, it does colonize and proliferate to high numbers in the kidneys. By combining mutations in the various iron acquisition loci (isd, fhuC, sst-1, and feo), we demonstrate that only a strain deficient for all of these systems was attenuated in its ability to proliferate to high numbers in the murine kidney. We propose the concerted action of heme and non-heme iron acquisition systems also enable S. lugdunensis to cause human infection.
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158
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Oral and external intervention on the crosstalk between microbial barrier and skin via foodborne functional component. J Funct Foods 2022. [DOI: 10.1016/j.jff.2022.105075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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159
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Zhu Y, Li P, Liu C, Jia M, Luo Y, He D, Liao C, Zhang S. Azobenzene quaternary ammonium salt for photo-controlled and reusable disinfection without drug resistance. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.05.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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160
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Marvasi M, Monici M, Pantalone D, Cavalieri D. Exploitation of Skin Microbiota in Wound Healing: Perspectives During Space Missions. Front Bioeng Biotechnol 2022; 10:873384. [PMID: 35573226 PMCID: PMC9098812 DOI: 10.3389/fbioe.2022.873384] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/11/2022] [Indexed: 01/05/2023] Open
Abstract
Wound healing is slowed in Space. Microgravity and possible physical factors associated with Space affect alterations in fibroblast, matrix formation, dysregulation in apoptosis and inflammation. The microbial populations settled on skin, space modules, in space suits, are also playing a pivotal role, as wound healing is also affected by the microbial community. We propose a perspective that includes four domines for the application of human skin microbiota for wound healing in Space: The natural antimicrobial properties of the skin microbiota, the crosstalk of the skin microbiota with the immune system during wound healing, the contribution of the microbiota in precision medicine, and the role of gut-skin and gut-brain axes. A stronger understanding of the connections and metabolic network among bacteria, fungi, the host’s immune system and the host metabolism will support the basis for a better wound healing in Space.
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Affiliation(s)
| | - Monica Monici
- ASAcampus Joint Laboratory, ASA Res. Div., Deptartment of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Desirée Pantalone
- Emergency Surgery Unit-Trauma Team, Emergency Department, Department of Experimental and Clinical Medicine, Careggi University Hospital, University of Florence, Florence, Italy
| | - Duccio Cavalieri
- Department of Biology, University of Florence, Florence, Italy
- *Correspondence: Duccio Cavalieri,
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161
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Cuthbert BJ, Hayes CS, Goulding CW. Functional and Structural Diversity of Bacterial Contact-Dependent Growth Inhibition Effectors. Front Mol Biosci 2022; 9:866854. [PMID: 35558562 PMCID: PMC9086364 DOI: 10.3389/fmolb.2022.866854] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/07/2022] [Indexed: 12/25/2022] Open
Abstract
Bacteria live in complex communities and environments, competing for space and nutrients. Within their niche habitats, bacteria have developed various inter-bacterial mechanisms to compete and communicate. One such mechanism is contact-dependent growth inhibition (CDI). CDI is found in many Gram-negative bacteria, including several pathogens. These CDI+ bacteria encode a CdiB/CdiA two-partner secretion system that delivers inhibitory toxins into neighboring cells upon contact. Toxin translocation results in the growth inhibition of closely related strains and provides a competitive advantage to the CDI+ bacteria. CdiB, an outer-membrane protein, secretes CdiA onto the surface of the CDI+ bacteria. When CdiA interacts with specific target-cell receptors, CdiA delivers its C-terminal toxin region (CdiA-CT) into the target-cell. CdiA-CT toxin proteins display a diverse range of toxic functions, such as DNase, RNase, or pore-forming toxin activity. CDI+ bacteria also encode an immunity protein, CdiI, that specifically binds and neutralizes its cognate CdiA-CT, protecting the CDI+ bacteria from auto-inhibition. In Gram-negative bacteria, toxin/immunity (CdiA-CT/CdiI) pairs have highly variable sequences and functions, with over 130 predicted divergent toxin/immunity complex families. In this review, we will discuss biochemical and structural advances made in the characterization of CDI. This review will focus on the diverse array of CDI toxin/immunity complex structures together with their distinct toxin functions. Additionally, we will discuss the most recent studies on target-cell recognition and toxin entry, along with the discovery of a new member of the CDI loci. Finally, we will offer insights into how these diverse toxin/immunity complexes could be harnessed to fight human diseases.
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Affiliation(s)
- Bonnie J. Cuthbert
- Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Christopher S. Hayes
- Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Celia W. Goulding
- Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, United States
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162
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Rocha GA, Ferreira RB. Antimicrobial polysaccharides obtained from natural sources. Future Microbiol 2022; 17:701-716. [PMID: 35392662 DOI: 10.2217/fmb-2021-0257] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
With the increase in resistance to conventional antibiotics among bacterial pathogens, the search for new antimicrobials becomes more and more necessary. Although most studies focus on the discovery of antimicrobial peptides for the development of new antibiotics, several others in the literature have described polysaccharides with the same biological activity with the potential for use as therapeutic alternatives. Here we review the currently available literature on antimicrobial polysaccharides isolated from different sources to demonstrate that there are several possible unconventional carbohydrate polymers that could act as therapeutic alternatives in the battle against drug-resistant pathogens.
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Affiliation(s)
- Giulia A Rocha
- Departamento de Microbiologia Médica Instituto de Microbiologia Paulo de Góes CCS, Bloco I2-028, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ, 21941-590, Brasil
| | - Rosana Br Ferreira
- Departamento de Microbiologia Médica Instituto de Microbiologia Paulo de Góes CCS, Bloco I2-028, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ, 21941-590, Brasil
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163
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Rehner J, Schmartz GP, Groeger L, Dastbaz J, Ludwig N, Hannig M, Rupf S, Seitz B, Flockerzi E, Berger T, Reichert MC, Krawczyk M, Meese E, Herr C, Bals R, Becker SL, Keller A, Müller R. Systematic Cross-biospecimen Evaluation of DNA Extraction Kits for Long- and Short-read Multi-metagenomic Sequencing Studies. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:405-417. [PMID: 35680095 PMCID: PMC9684153 DOI: 10.1016/j.gpb.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 05/13/2022] [Accepted: 05/19/2022] [Indexed: 01/05/2023]
Abstract
High-quality DNA extraction is a crucial step in metagenomic studies. Bias by different isolation kits impairs the comparison across datasets. A trending topic is, however, the analysis of multiple metagenomes from the same patients to draw a holistic picture of microbiota associated with diseases. We thus collected bile, stool, saliva, plaque, sputum, and conjunctival swab samples and performed DNA extraction with three commercial kits. For each combination of the specimen type and DNA extraction kit, 20-gigabase (Gb) metagenomic data were generated using short-read sequencing. While profiles of the specimen types showed close proximity to each other, we observed notable differences in the alpha diversity and composition of the microbiota depending on the DNA extraction kits. No kit outperformed all selected kits on every specimen. We reached consistently good results using the Qiagen QiAamp DNA Microbiome Kit. Depending on the specimen, our data indicate that over 10 Gb of sequencing data are required to achieve sufficient resolution, but DNA-based identification is superior to identification by mass spectrometry. Finally, long-read nanopore sequencing confirmed the results (correlation coefficient > 0.98). Our results thus suggest using a strategy with only one kit for studies aiming for a direct comparison of multiple microbiotas from the same patients.
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Affiliation(s)
- Jacqueline Rehner
- Institute of Medical Microbiology and Hygiene, Saarland University, D-66421 Homburg, Germany
| | | | - Laura Groeger
- Department of Human Genetics, Saarland University, D-66421 Homburg, Germany
| | - Jan Dastbaz
- Helmholtz Institute for Pharmaceutical Research Saarland, D-66123 Saarbrücken, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, D-66421 Homburg, Germany
| | - Matthias Hannig
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, D-66421 Homburg, Germany
| | - Stefan Rupf
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, D-66421 Homburg, Germany
| | - Berthold Seitz
- Department of Ophthalmology, Saarland University Medical Center, D-66421 Homburg, Germany
| | - Elias Flockerzi
- Department of Ophthalmology, Saarland University Medical Center, D-66421 Homburg, Germany
| | - Tim Berger
- Department of Ophthalmology, Saarland University Medical Center, D-66421 Homburg, Germany
| | | | - Marcin Krawczyk
- Department of Medicine II, Saarland University Medical Center, D-66421 Homburg, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, D-66421 Homburg, Germany
| | - Christian Herr
- Department of Internal Medicine V - Pulmonology, Allergology, Intensive Care Medicine, Saarland University, D-66421 Homburg, Germany
| | - Robert Bals
- Department of Internal Medicine V - Pulmonology, Allergology, Intensive Care Medicine, Saarland University, D-66421 Homburg, Germany
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, D-66421 Homburg, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, D-66123 Saarbrücken, Germany.
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, D-66123 Saarbrücken, Germany
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164
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Liu Y, Liu Q, Zhao L, Dickey SW, Wang H, Xu R, Chen T, Jian Y, Wang X, Lv H, Otto M, Li M. Essential role of membrane vesicles for biological activity of the bacteriocin micrococcin P1. J Extracell Vesicles 2022; 11:e12212. [PMID: 35384360 PMCID: PMC8982634 DOI: 10.1002/jev2.12212] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/17/2022] [Accepted: 03/19/2022] [Indexed: 11/12/2022] Open
Abstract
Bacterial membrane vesicles (MVs) have recently gained much attention and have been shown to carry a wide diversity of secreted bacterial components. However, it is poorly understood whether MV carriage is an indispensable requirement for a cargo's function. Bacteriocins as weapons of bacterial warfare shape the composition of microbial communities. Many bacteriocins have pronounced hydrophobicity that is imposed by their mechanism of action, but how they diffuse through aqueous environments to reach their target competitors is not known. Here we show that antimicrobial competitive activity of an exemplary hydrophobic bacteriocin of the thiopeptide antibiotic family, micrococcin P1 (MP1), is dependent on incorporation into MVs, which were found to carry MP1 at high concentrations. In contrast, MP1 without MV association was poorly active due to low solubility. Furthermore, we provide previously unavailable evidence that MVs fuse with a Gram-positive bacterium's cytoplasmic membrane, in this case to deliver a bacteriocin to its intracellular target. Our findings demonstrate how bacteria overcome the problem associated with secreting hydrophobic small molecules and delivering them to their target and show that MVs have a key function in bacterial warfare. Furthermore, our study provides hitherto rare evidence that MVs provide an essential rather than merely accessory function in bacterial physiology.
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Affiliation(s)
- Yao Liu
- Department of Laboratory MedicineRen Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Qian Liu
- Department of Laboratory MedicineRen Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Lu Zhao
- Research Center for Marine DrugsState Key Laboratory of Oncogenes and Related GenesDepartment of PharmacyRen Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Seth W. Dickey
- Pathogen Molecular Genetics SectionLaboratory of BacteriologyNational Institute of Allergy and Infectious DiseasesU.S. National Institutes of HealthBethesdaMarylandUSA
| | - Hua Wang
- Department of Laboratory MedicineRen Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Rui Xu
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineState Key Laboratory of Oncogenes and Related GenesRen Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Tianchi Chen
- Department of Laboratory MedicineRen Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Ying Jian
- Department of Laboratory MedicineRen Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xi Wang
- Department of Laboratory MedicineRen Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Huiying Lv
- Department of Laboratory MedicineRen Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Michael Otto
- Pathogen Molecular Genetics SectionLaboratory of BacteriologyNational Institute of Allergy and Infectious DiseasesU.S. National Institutes of HealthBethesdaMarylandUSA
| | - Min Li
- Department of Laboratory MedicineRen Ji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- Faculty of Medical LaboratoryScienceShanghai Jiao Tong University School of MedicineShanghaiChina
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165
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Diagne AM, Pelletier A, Durmort C, Faure A, Kanonenberg K, Freton C, Page A, Delolme F, Vorac J, Vallet S, Bellard L, Vivès C, Fieschi F, Vernet T, Rousselle P, Guiral S, Grangeasse C, Jault JM, Orelle C. Identification of a two-component regulatory system involved in antimicrobial peptide resistance in Streptococcus pneumoniae. PLoS Pathog 2022; 18:e1010458. [PMID: 35395062 PMCID: PMC9020739 DOI: 10.1371/journal.ppat.1010458] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 04/20/2022] [Accepted: 03/18/2022] [Indexed: 11/24/2022] Open
Abstract
Two-component regulatory systems (TCS) are among the most widespread mechanisms that bacteria use to sense and respond to environmental changes. In the human pathogen Streptococcus pneumoniae, a total of 13 TCS have been identified and many of them have been linked to pathogenicity. Notably, TCS01 strongly contributes to pneumococcal virulence in several infection models. However, it remains one of the least studied TCS in pneumococci and its functional role is still unclear. In this study, we demonstrate that TCS01 cooperates with a BceAB-type ABC transporter to sense and induce resistance to structurally-unrelated antimicrobial peptides of bacterial origin that all target undecaprenyl-pyrophosphate or lipid II, which are essential precursors of cell wall biosynthesis. Even though tcs01 and bceAB genes do not locate in the same gene cluster, disruption of either of them equally sensitized the bacterium to the same set of antimicrobial peptides. We show that the key function of TCS01 is to upregulate the expression of the transporter, while the latter appears the main actor in resistance. Electrophoretic mobility shift assays further demonstrated that the response regulator of TCS01 binds to the promoter region of the bceAB genes, implying a direct control of these genes. The BceAB transporter was overexpressed and purified from E. coli. After reconstitution in liposomes, it displayed substantial ATPase and GTPase activities that were stimulated by antimicrobial peptides to which it confers resistance to, revealing new functional features of a BceAB-type transporter. Altogether, this inducible defense mechanism likely contributes to the survival of the opportunistic microorganism in the human host, in which competition among commensal microorganisms is a key determinant for effective host colonization and invasive path.
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Affiliation(s)
- Aissatou Maty Diagne
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Anaïs Pelletier
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Claire Durmort
- Institute of Structural Biology (IBS), UMR 5075 CNRS/University of Grenoble-Alpes, Grenoble, France
| | - Agathe Faure
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Kerstin Kanonenberg
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Céline Freton
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Adeline Page
- Protein Science Facility, SFR BioSciences, CNRS, UMS3444, INSERM US8, University of Lyon, Lyon, France
| | - Frédéric Delolme
- Protein Science Facility, SFR BioSciences, CNRS, UMS3444, INSERM US8, University of Lyon, Lyon, France
| | - Jaroslav Vorac
- Institute of Structural Biology (IBS), UMR 5075 CNRS/University of Grenoble-Alpes, Grenoble, France
| | - Sylvain Vallet
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Laure Bellard
- Institute of Structural Biology (IBS), UMR 5075 CNRS/University of Grenoble-Alpes, Grenoble, France
| | - Corinne Vivès
- Institute of Structural Biology (IBS), UMR 5075 CNRS/University of Grenoble-Alpes, Grenoble, France
| | - Franck Fieschi
- Institute of Structural Biology (IBS), UMR 5075 CNRS/University of Grenoble-Alpes, Grenoble, France
| | - Thierry Vernet
- Institute of Structural Biology (IBS), UMR 5075 CNRS/University of Grenoble-Alpes, Grenoble, France
| | - Patricia Rousselle
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR 5305 CNRS/University of Lyon, Lyon, France
| | - Sébastien Guiral
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Jean-Michel Jault
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Cédric Orelle
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
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166
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Skin Microbiota in Atopic Dermatitis. Int J Mol Sci 2022; 23:ijms23073503. [PMID: 35408862 PMCID: PMC8998607 DOI: 10.3390/ijms23073503] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 12/26/2022] Open
Abstract
The skin microbiota represents an ecosystem composed of numerous microbial species interacting with each other, as well as with host epithelial and immune cells. The microbiota provides health benefits to the host by supporting essential functions of the skin and inhibiting colonization with pathogens. However, the disturbance of the microbial balance can result in dysbiosis and promote skin diseases, such as atopic dermatitis (AD). This review provides a current overview of the skin microbiota involvement in AD and its complex interplay with host immune response mechanisms, as well as novel therapeutic strategies for treating AD focused on restoring skin microbial homeostasis.
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167
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Ogura K, Furuya H, Takahashi N, Shibata K, Endo M, Watanabe S, Cui L, Miyoshi-Akiyama T, Okamoto S, Ogai K, Sugama J. Interspecies Regulation Between Staphylococcus caprae and Staphylococcus aureus Colonized on Healed Skin After Injury. Front Microbiol 2022; 13:818398. [PMID: 35300478 PMCID: PMC8921658 DOI: 10.3389/fmicb.2022.818398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/20/2022] [Indexed: 12/04/2022] Open
Abstract
Staphylococcus spp. colonize commensally on the human skin. Some commensal coagulase-negative staphylococci and Staphylococcus aureus are also involved in nosocomial infections. Bacteria were collected from skin healed from pressure injury (PI). After the collection time points, some patients suffered from recurrent PI (RPI). This study analyzed the characteristics of Staphylococcus spp. on healed skin before recurrence between healed skin that suffered from RPI within 6 weeks (RPI group) and healed skin that did not suffer within the duration (non-RPI group) by Staphylococcus spp.-specific sequencing. Of the seven patients in the RPI group, two were dominated by S. aureus and four by Staphylococcus caprae, coagulase-negative human commensal staphylococci in the RPI group. Using mouse models, both S. caprae and S. aureus, but not Staphylococcus epidermidis, colonized on skin healed from injury at significantly higher rates than normal skin. Although subcutaneous injection of S. caprae did not induce lesion formation, the bacterium exhibited high hemolytic activity on human red blood cells. Lesion formation by subcutaneous injection of S. aureus was significantly suppressed in the presence of S. caprae. The hemolytic activity of rabbit blood cells of S. aureus was suppressed by S. caprae, whereas the hemolytic activity of S. caprae was dramatically suppressed by S. aureus. Data indicated that each of the two Staphylococcus spp. suppresses the pathogenicity of the other and that the imbalance between the two is associated with RPI.
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Affiliation(s)
- Kohei Ogura
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Hiroka Furuya
- Department of Clinical Laboratory Science, Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Natsuki Takahashi
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Kana Shibata
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Maho Endo
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Shinya Watanabe
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Tohru Miyoshi-Akiyama
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Shinjuku, Japan
| | - Shigefumi Okamoto
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan.,Department of Clinical Laboratory Science, Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Kazuhiro Ogai
- AI Hospital/Macro Signal Dynamics Research and Development Center, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Junko Sugama
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan.,Research Center for Implementation Nursing Science Initiative, School of Health Sciences, Fujita Health University, Toyoake, Japan
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168
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Hemmerling F, Piel J. Strategies to access biosynthetic novelty in bacterial genomes for drug discovery. Nat Rev Drug Discov 2022; 21:359-378. [PMID: 35296832 DOI: 10.1038/s41573-022-00414-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2022] [Indexed: 12/17/2022]
Abstract
Bacteria provide a rich source of natural products with potential therapeutic applications, such as novel antibiotic classes or anticancer drugs. Bioactivity-guided screening of bacterial extracts and characterization of biosynthetic pathways for drug discovery is now complemented by the availability of large (meta)genomic collections, placing researchers into the postgenomic, big-data era. The progress in next-generation sequencing and the rise of powerful computational tools provide unprecedented insights into unexplored taxa, ecological niches and 'biosynthetic dark matter', revealing diverse and chemically distinct natural products in previously unstudied bacteria. In this Review, we discuss such sources of new chemical entities and the implications for drug discovery with a particular focus on the strategies that have emerged in recent years to identify and access novelty.
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Affiliation(s)
- Franziska Hemmerling
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland.
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169
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Platanus hybrida’s Phenolic Profile, Antioxidant Power, and Antibacterial Activity against Methicillin-Resistant Staphylococcus aureus (MRSA). HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8030243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Methicillin-resistant S. aureus (MRSA) are a threat to public health as they frequently reveal a multidrug-resistant pattern. Researchers all over the world are on an urgent hunt for new treatments to help fight infections before antibiotics become obsolete, and some natural alternatives, such as polyphenols, have already exhibited therapeutic properties. Therefore, this study aimed to determine the phenolic profile, antioxidant capacity, and antimicrobial activity against MRSA of the leaf, fruit, and stem bark extracts of Platanus hybrida. The polyphenols were extracted with a water/ethanol (20:80) mixture and the methodology included HPLC-DAD, DPPH, FRAP, and CuPRAC. To address this issue from a One Health perspective, the Kirby–Bauer disc diffusion method was performed against nine MRSA strains from three different sources (livestock, wild animals, and humans). Fourteen phenolics were identified and the leaf extract showed the highest phenolic content, followed by the fruit extract. The leaf extract also showed the highest antioxidant capacity while the fruit extract had the lowest antioxidant capacity. Both leaf and fruit extracts inhibited the growth of strains from all sources, while the stem bark extract did not inhibit the growth of human strains. This work highlights the complex chemical composition and the antioxidative and antimicrobial potential of extracts derived from P. hydrida.
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170
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Xie J, Tian S, Liu J, Cao R, Yue P, Cai X, Shang Q, Yang M, Han L, Zhang DK. Dual role of the nasal microbiota in neurological diseases—An unignorable risk factor or a potential therapy carrier. Pharmacol Res 2022; 179:106189. [DOI: 10.1016/j.phrs.2022.106189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/06/2022] [Accepted: 03/17/2022] [Indexed: 12/11/2022]
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171
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Konanov DN, Krivonos DV, Ilina EN, Babenko VV. BioCAT: search for biosynthetic gene clusters producing nonribosomal peptides with known structure. Comput Struct Biotechnol J 2022; 20:1218-1226. [PMID: 35317229 PMCID: PMC8914306 DOI: 10.1016/j.csbj.2022.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/14/2022] [Accepted: 02/14/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Dmitry N. Konanov
- Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical and Biological Agency of Russia, ul. Malaya Pirogovskaya., 1s3, Moscow 119435, Russian Federation
- Corresponding author.
| | - Danil V. Krivonos
- Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical and Biological Agency of Russia, ul. Malaya Pirogovskaya., 1s3, Moscow 119435, Russian Federation
| | - Elena N. Ilina
- Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical and Biological Agency of Russia, ul. Malaya Pirogovskaya., 1s3, Moscow 119435, Russian Federation
| | - Vladislav V. Babenko
- Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical and Biological Agency of Russia, ul. Malaya Pirogovskaya., 1s3, Moscow 119435, Russian Federation
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172
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Ortega-Peña S, Rodríguez-Martínez S, Cancino-Diaz ME, Cancino-Diaz JC. Staphylococcus epidermidis Controls Opportunistic Pathogens in the Nose, Could It Help to Regulate SARS-CoV-2 (COVID-19) Infection? Life (Basel) 2022; 12:341. [PMID: 35330092 PMCID: PMC8954679 DOI: 10.3390/life12030341] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/14/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Staphylococcus epidermidis is more abundant in the anterior nares than internal parts of the nose, but its relative abundance changes along with age; it is more abundant in adolescents than in children and adults. Various studies have shown that S. epidermidis is the guardian of the nasal cavity because it prevents the colonization and infection of respiratory pathogens (bacteria and viruses) through the secretion of antimicrobial molecules and inhibitors of biofilm formation, occupying the space of the membrane mucosa and through the stimulation of the host's innate and adaptive immunity. There is a strong relationship between the low number of S. epidermidis in the nasal cavity and the increased risk of serious respiratory infections. The direct application of S. epidermidis into the nasal cavity could be an effective therapeutic strategy to prevent respiratory infections and to restore nasal cavity homeostasis. This review shows the mechanisms that S. epidermidis uses to eliminate respiratory pathogens from the nasal cavity, also S. epidermidis is proposed to be used as a probiotic to prevent the development of COVID-19 because S. epidermidis induces the production of interferon type I and III and decreases the expression of the entry receptors of SARS-CoV-2 (ACE2 and TMPRSS2) in the nasal epithelial cells.
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Affiliation(s)
- Silvestre Ortega-Peña
- Laboratorio Tejido Conjuntivo, Centro Nacional de Investigación y Atención de Quemados, Instituto Nacional de Rehabilitación “Luís Guillermo Ibarra Ibarra”, Ciudad de México 14389, Mexico
| | - Sandra Rodríguez-Martínez
- Laboratorio de Inmunidad Innata, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (S.R.-M.); (M.E.C.-D.)
| | - Mario E. Cancino-Diaz
- Laboratorio de Inmunidad Innata, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (S.R.-M.); (M.E.C.-D.)
| | - Juan C. Cancino-Diaz
- Laboratorio de Inmunomicrobiología, Departamento Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
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173
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Ngo QV, Faass L, Sähr A, Hildebrand D, Eigenbrod T, Heeg K, Nurjadi D. Inflammatory Response Against Staphylococcus aureus via Intracellular Sensing of Nucleic Acids in Keratinocytes. Front Immunol 2022; 13:828626. [PMID: 35281009 PMCID: PMC8907419 DOI: 10.3389/fimmu.2022.828626] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/07/2022] [Indexed: 12/02/2022] Open
Abstract
Staphylococcus aureus is one of the clinically most relevant pathogens causing infections. Humans are often exposed to S. aureus. In approximately one-third of the healthy population it can be found on the skin either for long or short periods as colonizing "commensals", without inducing infections or an inflammatory immune response. While tolerating S. aureus seems to be limited to certain individuals and time periods in most cases, Staphylococcus epidermidis is tolerated permanently on the skin of almost all individuals without activating overwhelming skin inflammation. To investigate this, we co-cultured a keratinocyte cell line (HaCaT) with viable S. aureus or S. epidermidis to study the differences in the immune activation. S. aureus activated keratinocytes depicted by a profound IL-6 and IL-8 response, whereas S. epidermidis did not. Our data indicate that internalization of S. aureus and the subsequent intracellular sensing of bacterial nucleic acid may be essential for initiating inflammatory response in keratinocytes. Internalized dsRNA activates IL-6 and IL-8 release, but not TNF-α or IFNs by human keratinocytes. This is a non-specific effect of dsRNA, which can be induced using Poly(I:C), as well as RNA from S. aureus and S. epidermidis. However, only viable S. aureus were able to induce this response as these bacteria and not S. epidermidis were actively internalized by HaCaT. The stimulatory effect of S. aureus seems to be independent of the TLR3, -7 and -8 pathways.
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Affiliation(s)
- Quang Vinh Ngo
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Department of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Larissa Faass
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
- Max von Pettenkofer Institute, Chair for Medical Microbiology and Hygiene, Ludwig Maximilians University Munich, Munich, Germany
| | - Aline Sähr
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
| | - Dagmar Hildebrand
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
| | - Tatjana Eigenbrod
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
| | - Klaus Heeg
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Department of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Dennis Nurjadi
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Department of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
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174
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Liu L, Kirst ME, Zhao L, Li E, Wang GP. Microbiome Resilience despite a Profound Loss of Minority Microbiota following Clindamycin Challenge in Humanized Gnotobiotic Mice. Microbiol Spectr 2022; 10:e0196021. [PMID: 35019780 PMCID: PMC8754120 DOI: 10.1128/spectrum.01960-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 12/09/2021] [Indexed: 02/08/2023] Open
Abstract
Antibiotics are known to induce gut dysbiosis and increase the risk of antibiotic resistance. While antibiotic exposure is a known risk factor leading to compromised colonization resistance against enteric pathogens such as Clostridioides difficile, the extent and consequences of antibiotic perturbation on the human gut microbiome remain poorly understood. Human studies on impacts of antibiotics are complicated by the tremendous variability of gut microbiome among individuals, even between identical twins. Furthermore, antibiotic challenge experiments cannot be replicated in human subjects for a given gut microbiome. Here, we transplanted feces from three unrelated human donors into groups of identical germfree (GF) Swiss-Webster mice, and examined the temporal responses of the transplanted microbiome to oral clindamycin challenge in gnotobiotic isolators over 7 weeks. Analysis of 177 longitudinal fecal samples revealed that 59% to 81% of human microbiota established a stable configuration rapidly and stably in GF mice. Microbiome responses to clindamycin challenge was highly reproducible and microbiome-dependent. A short course of clindamycin was sufficient to induce a profound loss (∼one third) of the microbiota by disproportionally eliminating minority members of the transplanted microbiota. However, it was inadequate to disrupt the global microbial community structure or function, which rebounded rapidly to resemble its pre-treatment state after clindamycin discontinuation. Furthermore, the response of individual microbes was community-dependent. Taken together, these results suggest that the overall gut microbiome structure is resilient to antibiotic perturbation, the functional consequences of which warrant further investigation. IMPORTANCE Antibiotics cause imbalance of gut microbiota, which in turn increase our susceptibility to gastrointestinal infections. However, how antibiotics disrupt gut bacterial communities is not well understood, and exposing healthy volunteers to unnecessary antibiotics for research purposes carries clinical and ethical concerns. In this study, we used genetically identical mice transplanted with the same human gut microbiota to control for both genetic and environmental variables. We found that a short course of oral clindamycin was sufficient to eliminate one third of the gut bacteria by disproportionally eliminating minority members of the transplanted microbiota, but it was inadequate to disrupt the overall microbial community structure and function, which rebounded rapidly to its pre-treatment state. These results suggest that gut microbiome is highly resilient to antibiotic challenge and degradation of the human gut ecosystem may require repeated or prolonged antibiotic exposure.
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Affiliation(s)
- Lin Liu
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Mariana E. Kirst
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Lisa Zhao
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Eric Li
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Gary P. Wang
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
- North Florida/South Georgia Veterans Health System, Gainesville, Florida, USA
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175
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Khabthani S, Rolain JM, Merhej V. Whole Genome Analysis of 335 New Bacterial Species from Human Microbiota Reveals a Huge Reservoir of Transferable Antibiotic Resistance Determinants. Int J Mol Sci 2022; 23:ijms23042137. [PMID: 35216256 PMCID: PMC8874588 DOI: 10.3390/ijms23042137] [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: 12/28/2021] [Revised: 02/06/2022] [Accepted: 02/12/2022] [Indexed: 02/04/2023] Open
Abstract
Background: The emergence and diffusion of strains of pathogenic bacteria resistant to antibiotics constitutes a real public health challenge. Antibiotic resistance genes (ARGs) can be carried by both pathogenic and non-pathogenic bacteria, including commensal bacteria from the human microbiota, which require special monitoring in the fight against antimicrobial resistance. Methods: We analyzed the proteomes of 335 new bacterial species from human microbiota to estimate its whole range of ARGs using the BLAST program against ARGs reference databases. Results: We found 278 bacteria that harbor a total of 883 potential ARGs with the following distribution: 264 macrolides-lincosamides-streptogramin, 195 aminoglycosides, 156 tetracyclines, 58 β-lactamases, 58 fosfomycin, 51 glycopeptides, 36 nitroimidazoles, 33 phenicols and 32 rifamycin. Furthermore, evolutionary analyses revealed the potential horizontal transfer with pathogenic bacteria involving mobile genetic elements such as transposase and plasmid. We identified many ARGs that may represent new variants in fosfomycin and β-lactams resistance. Conclusion: These findings show that new bacterial species from human microbiota should be considered as an important reservoir of ARGs that can be transferred to pathogenic bacteria. In vitro analyses of their phenotypic potential are required to improve our understanding of the functional role of this bacterial community in the development of antibiotic resistance.
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Affiliation(s)
- Sami Khabthani
- Faculté de Pharmacie, Aix-Marseille Université, 13005 Marseille, France; (S.K.); (J.-M.R.)
- IHU Méditerranée Infection, Institut de Recherche Pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Jean-Marc Rolain
- Faculté de Pharmacie, Aix-Marseille Université, 13005 Marseille, France; (S.K.); (J.-M.R.)
- IHU Méditerranée Infection, Institut de Recherche Pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Vicky Merhej
- IHU Méditerranée Infection, Institut de Recherche Pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- Faculté de Sciences Médicales et Paramédicales, Aix-Marseille Université, 13005 Marseille, France
- Correspondence:
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176
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Abstract
Acinetobacter baumannii is an important hospital-associated pathogen that causes antibiotic resistant infections and reoccurring hospital outbreaks. A. baumannii’s ability to asymptomatically colonize patients is a risk factor for infection and exacerbates its spread. However, there is little information describing the mechanisms it employs to colonize patients. A. baumannii often colonizes the upper respiratory tract and skin. Antibiotic use is a risk factor for colonization and infection suggesting that A. baumannii likely competes with commensal bacteria to establish a niche. To begin to investigate this possibility, we cocultured A. baumannii and commensal bacteria of the upper respiratory tract and skin. In conditions that mimic iron starvation experienced in the host, we observed that A. baumannii inhibits Staphylococcus epidermidis, Staphylococcus hominis, Staphylococcus haemolyticus and Corynebacterium striatum. Then using an ordered transposon library screen we identified the A. baumannii siderophore acinetobactin as the causative agent of the inhibition phenotype. Using mass spectrometry, we show that acinetobactin is released from A. baumannii under our coculture conditions and that purified acinetobactin can inhibit C. striatum and S. hominis. Together our data suggest that acinetobactin may provide a competitive advantage for A. baumannii over some respiratory track and skin commensal bacteria and possibly support its ability to colonize patients. IMPORTANCE The ability of Acinetobacter baumannii to asymptomatically colonize patients is a risk factor for infection and exacerbates its clinical spread. However, there is minimal information describing how A. baumannii asymptomatically colonizes patients. Here we provide evidence that A. baumannii can inhibit the growth of many skin and upper respiratory commensal bacteria through iron competition and identify acinetobactin as the molecule supporting its nutritional advantage. Outcompeting endogenous commensals through iron competition may support the ability of A. baumannii to colonize and spread among patients.
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177
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Shetty SA, van Beek J, Bijvank E, Groot J, Kuiling S, Bosch T, van Baarle D, Fuentes S. Associations and recovery dynamics of the nasopharyngeal microbiota during influenza-like illness in the aging population. Sci Rep 2022; 12:1915. [PMID: 35115596 PMCID: PMC8813934 DOI: 10.1038/s41598-022-05618-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/12/2022] [Indexed: 11/09/2022] Open
Abstract
Influenza-like illness (ILI), a disease caused by respiratory pathogens including influenza virus, is a major health concern in older adults. There is little information on changes and recovery dynamics of the nasopharyngeal (NP) microbiota of older adults associated with an ILI. Here, we compared the NP microbiota in older adults reporting (n = 240) or not (n = 157) ILI during the 2014-2015 influenza season at different times of the ILI event. A small but significant effect of the ILI was observed on the microbiota community composition and structure when compared to controls and samples collected at recovery. Corynebacterium was negatively associated with ILI and its abundance increased after recovery. Potential pathobionts such as Haemophilus, Porphyromonas and Gemella had higher abundances during acute-ILI. Stability and changes in the NP microbial community showed individual dynamics. Key core genera, Corynebacterium, Moraxella and Dolosigranulum exhibited higher inter-individual variability in acute-ILI, but showed comparable variability to controls after recovery. Participants in the ILI group with higher core microbiota abundances at the acute phase showed higher microbiota stability after recovery. Our findings demonstrate that acute-ILI is associated with alterations in the phylogenetic structure of the NP microbiota in older adults. The variation in the core microbiota suggests imbalances in the ecosystem, which could potentially play a role in the susceptibility and recovery of the NP microbiota after an ILI event.
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Affiliation(s)
- Sudarshan A Shetty
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Department of Medical Microbiology and Infection Prevention, Virology and Immunology Research Group, University Medical Center Groningen, Groningen, The Netherlands
| | - Josine van Beek
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Elske Bijvank
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - James Groot
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Sjoerd Kuiling
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Thijs Bosch
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Debbie van Baarle
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Department of Medical Microbiology and Infection Prevention, Virology and Immunology Research Group, University Medical Center Groningen, Groningen, The Netherlands
| | - Susana Fuentes
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands.
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178
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Molecular Diagnosis, Antimicrobial Resistance Profiles and Disease Patterns of Gram-Positive Pathogens Recovered from Clinical Infections in Major Ha’il Hospitals. MICROBIOLOGY RESEARCH 2022. [DOI: 10.3390/microbiolres13010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Nosocomial resistance in staphylococci and enterococci is challenging. The aim of this work was to conduct a multipoint study using molecular detections, antimicrobial resistances profiles, patient demographics and disease patterns for objective assessments of Staphilococcus aureus and other Gram-positive pathogens recovered from clinical infections in the Ha’il region. We have surveyed 188 non-duplicate Gram-positives against 22 antimicrobials for molecular-differentiation, resistance, patient demographics, and disease patterns from January–April 2021. According to definitions for acquired resistance, Staphylococcus aureus was the most frequent with multidrug resistant (65.4%), where MRSA was 60% (n = 72 out of 121). In age-identified patients, 43% were seniors ≥50 years, 38% 21–49 years, and 19% 0–20 years. In gender-identified patients, 63% were males, and 37% were females. While 25% of specimens were from the ICU, the majority (60%) of specimens were from surgical infection in other wards. Staphylococcus epidermidis was the second (15.4%) species of infection identified with 81% from bloodstream infections at the ICU and other wards. The majority of S. epidermidis patients (69%) were seniors ≥50 years, while other age groups 0–20 and 21–49 each had 14% isolates. Although S. epidermidis was multidrug-resistant, it was susceptible to many drugs. Enterococcus faecalis (13%) ranked third with two major infections; bloodstream (64%) and urinary-tract infections (36%) in mainly seniors (86%). Its isolates were fully resistant to oxacillin, penicillin, cefoxitin, and cefotaxime but nearly 100% susceptible to seven others. Other Gram-positive bacteria (6%) were susceptible to many antibiotics. The use of combinations of objective criteria is a well thought out approach in infection control. While the low-frequency of Gram-positives is an impressive achievement, future large-scale investigations should include all private hospitals, clinics and other cities over a longer sampling time to gain more insights. Although geriatric susceptibility can be justified by age and comorbidities, the staphylococcal infections in young adults and children is a global concern and warrants more vertical studies.
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179
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Randall JR, Davidson G, Fleeman RM, Acosta SA, Riddington IM, Cole TJ, DuPai CD, Davies BW. Synthetic antibacterial discovery of symbah-1, a macrocyclic β-hairpin peptide antibiotic. iScience 2022; 25:103611. [PMID: 35005555 PMCID: PMC8719016 DOI: 10.1016/j.isci.2021.103611] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/16/2021] [Accepted: 12/08/2021] [Indexed: 12/14/2022] Open
Abstract
The rapid development and spread of antibiotic resistance necessitate the development of novel strategies for antibiotic discovery. Symbah-1, a synthetic peptide antibiotic, was identified in a high-throughput antibacterial screen of random peptide sequences. Symbah-1 functions through membrane disruption and contains broad spectrum bactericidal activity against several drug-resistant pathogens. Circular dichroism and high-resolution mass spectrometry indicate symbah-1 has a β-hairpin structure induced by lipopolysaccharide and is cyclized via an intramolecular disulfide bond. Together these data classify symbah-1 as an uncommon synthetic member of the β-hairpin antimicrobial peptide class. Symbah-1 displays low hemolysis but loses activity in human serum. Characterization of a symbah-1 peptide library identified two variants with increased serum activity and protease resistance. The method of discovery and subsequent characterization of symbah-1 suggests large synthetic peptide libraries bias toward macrocyclic β-hairpin structure could be designed and screened to rapidly expand and better understand this rare peptide antibiotic class.
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Affiliation(s)
- Justin R. Randall
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Gillian Davidson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Renee M. Fleeman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Santos A. Acosta
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Ian M. Riddington
- Mass Spectrometry Facility, Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - T. Jeffrey Cole
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Cory D. DuPai
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Bryan W. Davies
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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180
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Carpa R, Remizovschi A, Culda CA, Butiuc-Keul AL. Inherent and Composite Hydrogels as Promising Materials to Limit Antimicrobial Resistance. Gels 2022; 8:70. [PMID: 35200452 PMCID: PMC8870943 DOI: 10.3390/gels8020070] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/22/2021] [Accepted: 01/11/2022] [Indexed: 01/25/2023] Open
Abstract
Antibiotic resistance has increased significantly in the recent years, and has become a global problem for human health and the environment. As a result, several technologies for the controlling of health-care associated infections have been developed over the years. Thus, the most recent findings in hydrogel fabrication, particularly antimicrobial hydrogels, could offer valuable solutions for these biomedical challenges. In this review, we discuss the most promising strategies in the development of antimicrobial hydrogels and the application of hydrogels in the treatment of microbial infections. The latest advances in the development of inherently and composite antimicrobial hydrogels will be discussed, as well as hydrogels as carriers of antimicrobials, with a focus on antibiotics, metal nanoparticles, antimicrobial peptides, and biological extracts. The emergence of CRISR-Cas9 technology for removing the antimicrobial resistance has led the necessity of new and performant carriers for delivery of the CRISPR-Cas9 system. Different delivery systems, such as composite hydrogels and many types of nanoparticles, attracted a great deal of attention and will be also discussed in this review.
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Affiliation(s)
- Rahela Carpa
- Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University, 1 M. Kogalniceanu Street, 400084 Cluj-Napoca, Romania; (R.C.); (A.L.B.-K.)
- Center of Systems Biology, Biodiversity and Bioresources, Babeş-Bolyai University, 5-7 Clinicilor Street, 400006 Cluj-Napoca, Romania
| | - Alexei Remizovschi
- Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University, 1 M. Kogalniceanu Street, 400084 Cluj-Napoca, Romania; (R.C.); (A.L.B.-K.)
- Center of Systems Biology, Biodiversity and Bioresources, Babeş-Bolyai University, 5-7 Clinicilor Street, 400006 Cluj-Napoca, Romania
| | - Carla Andreea Culda
- Parasitology and Parasitic Diseases Department, University of Agricultural Sciences and Veterinary Medicine, 3-5 Calea Manastur Street, 400372 Cluj-Napoca, Romania;
| | - Anca Livia Butiuc-Keul
- Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University, 1 M. Kogalniceanu Street, 400084 Cluj-Napoca, Romania; (R.C.); (A.L.B.-K.)
- Center of Systems Biology, Biodiversity and Bioresources, Babeş-Bolyai University, 5-7 Clinicilor Street, 400006 Cluj-Napoca, Romania
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181
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Wuethrich I, W. Pelzer B, Khodamoradi Y, Vehreschild MJGT. The role of the human gut microbiota in colonization and infection with multidrug-resistant bacteria. Gut Microbes 2022; 13:1-13. [PMID: 33870869 PMCID: PMC8078746 DOI: 10.1080/19490976.2021.1911279] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
About 100 years ago, the first antibiotic drug was introduced into health care. Since then, antibiotics have made an outstanding impact on human medicine. However, our society increasingly suffers from collateral damage exerted by these highly effective drugs. The rise of resistant pathogen strains, combined with a reduction of microbiota diversity upon antibiotic treatment, has become a significant obstacle in the fight against invasive infections worldwide.Alternative and complementary strategies to classical "Fleming antibiotics" comprise microbiota-based treatments such as fecal microbiota transfer and administration of probiotics, live-biotherapeutics, prebiotics, and postbiotics. Other promising interventions, whose efficacy may also be influenced by the human microbiota, are phages and vaccines. They will facilitate antimicrobial stewardship, to date the only globally applied antibiotic resistance mitigation strategy.In this review, we present the available evidence on these nontraditional interventions, highlight their interaction with the human microbiota, and discuss their clinical applicability.
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Affiliation(s)
- Irene Wuethrich
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Benedikt W. Pelzer
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Department I of Internal Medicine, University of Cologne, Cologne, Germany
| | - Yascha Khodamoradi
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt Am Main, Germany
| | - Maria J. G. T. Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt Am Main, Germany,CONTACT Maria J. G. T. Vehreschild Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt Am Main, Germany
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182
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Abstract
Natural products offer an important avenue to novel therapeutics against drug-resistant bacteria, viruses, fungi, parasites, and cancer. However, there are numerous hurdles and challenges in discovering such molecules, including antimicrobial peptides (AMPs). While a thorough characterization of AMPs is limited by the amount of material, existing technology, and researcher's expertise, peptide classification is complicated by incomplete information as well as different methods proposed for AMPs from bacteria, plants, and animals. This article describes unified classification schemes for natural AMPs on a common platform: the Antimicrobial Peptide Database (APD; https://aps.unmc.edu). The various criteria for these unified classifications include peptide biological source, biosynthesis machinery, biological activity, amino acid sequence, mechanism of action, and three-dimensional structure. To overcome the problem with a limited number of known 3D structures, a universal peptide classification has also been refined and executed in the APD database. This universal method, based on the spatial connection patterns of polypeptide chains, is independent of peptide source, size, activity, 3D structure, or mechanism of action. It facilitates information registration, naming, exchange, decoding, prediction, and design of novel antimicrobial peptides.
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183
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Abstract
The skin microbiome is a key component of pathogenesis in atopic dermatitis (AD). The skin of AD patients is characterized by microbial dysbiosis, with a reduction of microbial diversity and overrepresentation of pathogenic Staphylococcus aureus (S. aureus). Recent exciting studies have elucidated an importance of establishing an appropriate immune response to microbes in early life and uncovered the new mechanisms of microbial community dynamics in modulating our skin microbiome. Several microbes are associated with AD pathogenesis, with proposed pathogenic effects from S. aureus and Malassezia. The complex relationships between microbes within the skin microbiome consortia includes various species, such as Staphylococcal, Roseomonas and Cutibacterium strains, that can inhibit S. aureus and are potential probiotics for AD skin. Numerous microbes are now also reported to modulate host response via communication with keratinocytes, specialized immune cells and adipocytes to improve skin health and barrier function. This increased understanding of skin microbiota bioactives has led to new biotherapeutic approaches that target the skin surface microenvironment for AD treatment.
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184
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Wang G, Zietz CM, Mudgapalli A, Wang S, Wang Z. The evolution of the antimicrobial peptide database over 18 years: Milestones and new features. Protein Sci 2022; 31:92-106. [PMID: 34529321 PMCID: PMC8740828 DOI: 10.1002/pro.4185] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/03/2021] [Accepted: 09/03/2021] [Indexed: 01/03/2023]
Abstract
The antimicrobial peptide database (APD) has served the antimicrobial peptide field for 18 years. Because it is widely used in research and education, this article documents database milestones and key events that have transformed it into the current form. A comparison is made for the APD peptide statistics between 2010 and 2020, validating the major database findings to date. We also describe new additions ranging from peptide entries to search functions. Of note, the APD also contains antimicrobial peptides from host microbiota, which are important in shaping immune systems and could be linked to a variety of human diseases. Finally, the database has been re-programmed to the web branding and latest security compliance of the University of Nebraska Medical Center. The reprogrammed APD can be accessed at https://aps.unmc.edu.
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Affiliation(s)
- Guangshun Wang
- Department of Pathology and MicrobiologyCollege of Medicine, University of Nebraska Medical Center, 985900 Nebraska Medical CenterOmahaNebraskaUSA
| | - C. Michael Zietz
- Research Information Technology OfficeUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Ashok Mudgapalli
- Research Information Technology OfficeUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Shuona Wang
- Department of Pathology and MicrobiologyCollege of Medicine, University of Nebraska Medical Center, 985900 Nebraska Medical CenterOmahaNebraskaUSA
| | - Zhe Wang
- Department of Pathology and MicrobiologyCollege of Medicine, University of Nebraska Medical Center, 985900 Nebraska Medical CenterOmahaNebraskaUSA
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185
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Song A, Lee SE, Kim JH. Immunopathology and Immunotherapy of Inflammatory Skin Diseases. Immune Netw 2022; 22:e7. [PMID: 35291649 PMCID: PMC8901701 DOI: 10.4110/in.2022.22.e7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/20/2022] [Accepted: 01/23/2022] [Indexed: 12/01/2022] Open
Abstract
Recently, there have been impressive advancements in understanding of the immune mechanisms underlying cutaneous inflammatory diseases. To understand these diseases on a deeper level and clarify the therapeutic targets more precisely, numerous studies including in vitro experiments, animal models, and clinical trials have been conducted. This has resulted in a paradigm shift from non-specific suppression of the immune system to selective, targeted immunotherapies. These approaches target the molecular pathways and cytokines responsible for generating inflammatory conditions and reinforcing feedback mechanisms to aggravate inflammation. Among the numerous types of skin inflammation, psoriasis and atopic dermatitis (AD) are common chronic cutaneous inflammatory diseases. Psoriasis is a IL-17–mediated disease driven by IL-23, while AD is predominantly mediated by Th2 immunity. Autoimmune bullous diseases are autoantibody-mediated blistering disorders, including pemphigus and bullous pemphigoid. Alopecia areata is an organ-specific autoimmune disease mediated by CD8+ T-cells that targets hair follicles. This review will give an updated, comprehensive summary of the pathophysiology and immune mechanisms of inflammatory skin diseases. Moreover, the therapeutic potential of current and upcoming immunotherapies will be discussed.
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Affiliation(s)
- Ahreum Song
- Department of Dermatology, Gangnam Severance Hospital, Cutaneous Biology Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Sang Eun Lee
- Department of Dermatology, Gangnam Severance Hospital, Cutaneous Biology Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Jong Hoon Kim
- Department of Dermatology, Gangnam Severance Hospital, Cutaneous Biology Research Institute, Yonsei University College of Medicine, Seoul, Korea
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186
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Ding Y, Wang ZY, Ren ZW, Zhang XW, Wei D. Advances in Modified Hyaluronic Acid-Based Hydrogels for Skin Wound Healing. Biomater Sci 2022; 10:3393-3409. [DOI: 10.1039/d2bm00397j] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hyaluronic acid (HA) is a natural linear anionic polysaccharide with many unique characteristics such as excellent biocompatibility and biodegradability, native biofunctionality, hydrophilicity, and non-immunoreactivity. HA plays crucial roles in numerous...
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187
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Shi J, Ma JQ, Wang YC, Xu ZF, Zhang B, Jiao RH, Tan RX, Ge HM. Discovery of daspyromycins A and B, 2-aminovinyl-cysteine containing lanthipeptides, through a genomics-based approach. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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188
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Next-generation microbial drugs developed from microbiome's natural products. ADVANCES IN GENETICS 2021; 108:341-382. [PMID: 34844715 DOI: 10.1016/bs.adgen.2021.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Scientists working in natural products chemistry have been enticed by the current advancements being made in the discovery of novel "magic bullets" from microbes homed to all conceivable environments. Even though researchers continue to face challenges funneling the novel bioactive compounds in the global therapeutic industries, it seems most likely that the discovery of some "hit molecules" with significant biomedical applications is not that far. We applaud novel natural products for their ability to combat the spread of superbugs and aid in the prevention of currently observed antibiotic resistance. This in-depth investigation covers a wide range of microbiomes with a proclivity for synthesizing novel compounds to combat the spread of superbugs. Furthermore, we use this opportunity to explore various groups of secondary metabolites and their biosynthetic pathways in various microbiota found in mammals, insects, and humans. This systematic study, when taken as a whole, offers detail understanding on the biomedical fate of various groups of compounds originated from diverse microbiomes. For gathering all information that has been uncovered and released so far, we have also presented the huge diversity of microbes that are associated with humans and their metabolic products. To conclude, this concrete review suggests novel ideas that will prove immensely helpful in reducing the danger posed by superbugs while also improving the efficacy of antibiotics.
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189
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Darbandi A, Asadi A, Mahdizade Ari M, Ohadi E, Talebi M, Halaj Zadeh M, Darb Emamie A, Ghanavati R, Kakanj M. Bacteriocins: Properties and potential use as antimicrobials. J Clin Lab Anal 2021; 36:e24093. [PMID: 34851542 PMCID: PMC8761470 DOI: 10.1002/jcla.24093] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/03/2021] [Accepted: 10/24/2021] [Indexed: 12/12/2022] Open
Abstract
A variety of bacteriocins originate from lactic acid bacteria, which have recently been modified by scientists. Many strains of lactic acid bacteria related to food groups could produce bacteriocins or antibacterial proteins highly effective against foodborne pathogens such as Staphylococcus aureus, Pseudomonas fluorescens, P. aeruginosa, Salmonella typhi, Shigella flexneri, Listeria monocytogenes, Escherichia coli O157:H7, and Clostridium botulinum. A wide range of bacteria belonging primarily to the genera Bifidobacterium and Lactobacillus have been characterized with different health‐promoting attributes. Extensive studies and in‐depth understanding of these antimicrobials mechanisms of action could enable scientists to determine their production in specific probiotic lactic acid bacteria, as they are potentially crucial for the final preservation of functional foods or for medicinal applications. In this review study, the structure, classification, mode of operation, safety, and antibacterial properties of bacteriocins as well as their effect on foodborne pathogens and antibiotic‐resistant bacteria were extensively studied.
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Affiliation(s)
- Atieh Darbandi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Arezoo Asadi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Marzieh Mahdizade Ari
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Elnaz Ohadi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Malihe Talebi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Masoume Halaj Zadeh
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Amir Darb Emamie
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Maryam Kakanj
- Food and Drug Laboratory Research Center, Food and Drug Administration, MOH&ME, Tehran, Iran
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190
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Yang J, Yu G, Sessler JL, Shin I, Gale PA, Huang F. Artificial transmembrane ion transporters as potential therapeutics. Chem 2021. [DOI: 10.1016/j.chempr.2021.10.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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191
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Chevrette MG, Handelsman J. Needles in haystacks: reevaluating old paradigms for the discovery of bacterial secondary metabolites. Nat Prod Rep 2021; 38:2083-2099. [PMID: 34693961 DOI: 10.1039/d1np00044f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2021Natural products research is in the midst of a renaissance ushered in by a modern understanding of microbiology and the technological explosions of genomics and metabolomics. As the exploration of uncharted chemical space expands into high-throughput discovery campaigns, it has become increasingly clear how design elements influence success: (bio)geography, habitat, community dynamics, culturing/induction methods, screening methods, dereplication, and more. We explore critical considerations and assumptions in natural products discovery. We revisit previous estimates of chemical rediscovery and discuss their relatedness to study design and producer taxonomy. Through frequency analyses of biosynthetic gene clusters in publicly available genomic data, we highlight phylogenetic biases that influence rediscovery rates. Through selected examples of how study design at each level determines discovery outcomes, we discuss the challenges and opportunities for the future of high-throughput natural product discovery.
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Affiliation(s)
- Marc G Chevrette
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA.
| | - Jo Handelsman
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA.
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192
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Synthetic Biology Advanced Natural Product Discovery. Metabolites 2021; 11:metabo11110785. [PMID: 34822443 PMCID: PMC8617713 DOI: 10.3390/metabo11110785] [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: 11/04/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 01/16/2023] Open
Abstract
A wide variety of bacteria, fungi and plants can produce bioactive secondary metabolites, which are often referred to as natural products. With the rapid development of DNA sequencing technology and bioinformatics, a large number of putative biosynthetic gene clusters have been reported. However, only a limited number of natural products have been discovered, as most biosynthetic gene clusters are not expressed or are expressed at extremely low levels under conventional laboratory conditions. With the rapid development of synthetic biology, advanced genome mining and engineering strategies have been reported and they provide new opportunities for discovery of natural products. This review discusses advances in recent years that can accelerate the design, build, test, and learn (DBTL) cycle of natural product discovery, and prospects trends and key challenges for future research directions.
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193
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Characterising clinical Staphylococcus aureus isolates from the sinuses of patients with chronic rhinosinusitis. Sci Rep 2021; 11:21940. [PMID: 34753993 PMCID: PMC8578559 DOI: 10.1038/s41598-021-01297-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/26/2021] [Indexed: 02/08/2023] Open
Abstract
The role of Staphylococcus aureus in the pathogenesis of the chronic sinonasal disease chronic rhinosinusitis (CRS), has not been definitively established. Comparative analyses of S. aureus isolates from CRS with those from control participants may offer insight into a possible pathogenic link between this organism and CRS. The intra- and inter-subject S. aureus strain-level diversity in the sinuses of patients with and without CRS were compared in this cross-sectional study. In total, 100 patients (CRS = 64, control = 36) were screened for S. aureus carriage. The overall carriage prevalence of S. aureus in this cohort was 24% (CRS n = 13, control n = 11). Cultured S. aureus isolates from 18 participants were strain-typed using spa gene sequencing. The bacterial community composition of the middle meatus was assessed using amplicon sequencing targeting the V3V4 hypervariable region of the bacterial 16S rRNA gene. S. aureus isolates cultured from patients were grown in co-culture with the commensal bacterium Dolosigranulum pigrum and characterised. All participants harboured a single S. aureus strain and no trend in disease-specific strain-level diversity was observed. Bacterial community analyses revealed a significant negative correlation in the relative abundances of S. aureus and D. pigrum sequences, suggesting an antagonistic interaction between these organisms. Co-cultivation experiments with these bacteria, however, did not confirm this interaction in vitro. We saw no significant associations of CRS disease with S. aureus strain types. The functional role that S. aureus occupies in CRS likely depends on other factors such as variations in gene expression and interactions with other members of the sinus bacterial community.
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194
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In Silico/In Vitro Strategies Leading to the Discovery of New Nonribosomal Peptide and Polyketide Antibiotics Active against Human Pathogens. Microorganisms 2021; 9:microorganisms9112297. [PMID: 34835423 PMCID: PMC8625390 DOI: 10.3390/microorganisms9112297] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 12/12/2022] Open
Abstract
Antibiotics are majorly important molecules for human health. Following the golden age of antibiotic discovery, a period of decline ensued, characterised by the rediscovery of the same molecules. At the same time, new culture techniques and high-throughput sequencing enabled the discovery of new microorganisms that represent a potential source of interesting new antimicrobial substances to explore. The aim of this review is to present recently discovered nonribosomal peptide (NRP) and polyketide (PK) molecules with antimicrobial activity against human pathogens. We highlight the different in silico/in vitro strategies and approaches that led to their discovery. As a result of technological progress and a better understanding of the NRP and PK synthesis mechanisms, these new antibiotic compounds provide an additional option in human medical treatment and a potential way out of the impasse of antibiotic resistance.
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195
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Wertman JN, Dunn KA, Kulkarni K. The impact of the host intestinal microbiome on carcinogenesis and the response to chemotherapy. Future Oncol 2021; 17:4371-4387. [PMID: 34448411 DOI: 10.2217/fon-2021-0087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The microbiome consists of all microbes present on and within the human body. An unbalanced, or 'dysbiotic' intestinal microbiome is associated with inflammatory bowel disease, diabetes and some cancer types. Drug treatment can alter the intestinal microbiome composition. Additionally, some chemotherapeutics interact with microbiome components, leading to changes in drug safety and/or efficacy. The intestinal microbiome is a modifiable target, using strategies such as antibiotic treatment, fecal microbial transplantation or probiotic administration. Understanding the impact of the microbiome on the safety and efficacy of cancer treatment may result in improved treatment outcome. The present review seeks to summarize relevant research and look to the future of cancer treatment, where the intestinal microbiome is recognized as an actionable treatment target.
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Affiliation(s)
- Jaime N Wertman
- Department of Pediatrics/Division of Pediatric Hematology-Oncology, Dalhousie University/IWK Health Centre, Halifax, Canada
- College of Pharmacy, Dalhousie University, Halifax, Canada
| | - Katherine A Dunn
- Department of Pediatrics/Division of Pediatric Hematology-Oncology, Dalhousie University/IWK Health Centre, Halifax, Canada
- Department of Biology, Dalhousie University, Halifax, Canada
| | - Ketan Kulkarni
- Department of Pediatrics/Division of Pediatric Hematology-Oncology, Dalhousie University/IWK Health Centre, Halifax, Canada
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196
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Heilbronner S, Krismer B, Brötz-Oesterhelt H, Peschel A. The microbiome-shaping roles of bacteriocins. Nat Rev Microbiol 2021; 19:726-739. [PMID: 34075213 DOI: 10.1038/s41579-021-00569-w] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2021] [Indexed: 02/05/2023]
Abstract
The microbiomes on human body surfaces affect health in multiple ways. They include not only commensal or mutualistic bacteria but also potentially pathogenic bacteria, which can enter sterile tissues to cause invasive infection. Many commensal bacteria produce small antibacterial molecules termed bacteriocins that have the capacity to eliminate specific colonizing pathogens; as such, bacteriocins have attracted increased attention as potential microbiome-editing tools. Metagenome-based and activity-based screening approaches have strongly expanded our knowledge of the abundance and diversity of bacteriocin biosynthetic gene clusters and the properties of a continuously growing list of bacteriocin classes. The dynamic acquisition, diversification or loss of bacteriocin genes can shape the fitness of a bacterial strain that is in competition with bacteriocin-susceptible bacteria. However, a bacteriocin can only provide a competitive advantage if its fitness benefit exceeds the metabolic cost of production, if it spares crucial mutualistic partner strains and if major competitors cannot develop resistance. In contrast to most currently available antibiotics, many bacteriocins have only narrow activity ranges and could be attractive agents for precision therapy and prevention of infections. A common scientific strategy involving multiple disciplines is needed to uncover the immense potential of microbiome-shaping bacteriocins.
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Affiliation(s)
- Simon Heilbronner
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany. .,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
| | - Bernhard Krismer
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, Department of Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany. .,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
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197
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Biogeography of Bacterial Communities and Specialized Metabolism in Human Aerodigestive Tract Microbiomes. Microbiol Spectr 2021; 9:e0166921. [PMID: 34704787 PMCID: PMC8549736 DOI: 10.1128/spectrum.01669-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The aerodigestive tract (ADT) is the primary portal through which pathogens and other invading microbes enter the body. As the direct interface with the environment, we hypothesize that the ADT microbiota possess biosynthetic gene clusters (BGCs) for antibiotics and other specialized metabolites to compete with both endogenous and exogenous microbes. From 1,214 bacterial genomes, representing 136 genera and 387 species that colonize the ADT, we identified 3,895 BGCs. To determine the distribution of BGCs and bacteria in different ADT sites, we aligned 1,424 metagenomes, from nine different ADT sites, onto the predicted BGCs. We show that alpha diversity varies across the ADT and that each site is associated with distinct bacterial communities and BGCs. We identify specific BGC families enriched in the buccal mucosa, external naris, gingiva, and tongue dorsum despite these sites harboring closely related bacteria. We reveal BGC enrichment patterns indicative of the ecology at each site. For instance, aryl polyene and resorcinol BGCs are enriched in the gingiva and tongue, which are colonized by many anaerobes. In addition, we find that streptococci colonizing the tongue and cheek possess different ribosomally synthesized and posttranslationally modified peptide BGCs. Finally, we highlight bacterial genera with BGCs but are underexplored for specialized metabolism and demonstrate the bioactivity of Actinomyces against other bacteria, including human pathogens. Together, our results demonstrate that specialized metabolism in the ADT is extensive and that by exploring these microbiomes further, we will better understand the ecology and biogeography of this system and identify new bioactive natural products. IMPORTANCE Bacteria produce specialized metabolites to compete with other microbes. Though the biological activities of many specialized metabolites have been determined, our understanding of their ecology is limited, particularly within the human microbiome. As the aerodigestive tract (ADT) faces the external environment, bacteria colonizing this tract must compete both among themselves and with invading microbes, including human pathogens. We analyzed the genomes of ADT bacteria to identify biosynthetic gene clusters (BGCs) for specialized metabolites. We found that the majority of ADT BGCs are uncharacterized and the metabolites they encode are unknown. We mapped the distribution of BGCs across the ADT and determined that each site is associated with its own distinct bacterial community and BGCs. By further characterizing these BGCs, we will inform our understanding of ecology and biogeography across the ADT, and we may uncover new specialized metabolites, including antibiotics.
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198
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Lavrinienko A, Scholier T, Bates ST, Miller AN, Watts PC. Defining gut mycobiota for wild animals: a need for caution in assigning authentic resident fungal taxa. Anim Microbiome 2021; 3:75. [PMID: 34711273 PMCID: PMC8554864 DOI: 10.1186/s42523-021-00134-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022] Open
Abstract
Animal gut mycobiota, the community of fungi that reside within the gastrointestinal tract, make an important contribution to host health. Accordingly, there is an emerging interest to quantify the gut mycobiota of wild animals. However, many studies of wild animal gut mycobiota do not distinguish between the fungi that likely can reside within animal gastrointestinal tracts from the fungal taxa that are non-residents, such as macrofungi, lichens or plant symbionts/pathogens that can be ingested as part of the host's diet. Confounding the non-resident and resident gut fungi may obscure attempts to identify processes associated with the authentic, resident gut mycobiota per se. To redress this problem, we propose some strategies to filter the taxa identified within an apparent gut mycobiota based on an assessment of host ecology and fungal traits. Consideration of the different sources and roles of fungi present within the gastrointestinal tract should facilitate a more precise understanding of the causes and consequences of variation in wild animal gut mycobiota composition.
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Affiliation(s)
- Anton Lavrinienko
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Tiffany Scholier
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Scott T Bates
- Department of Biological Sciences, Purdue University Northwest, Westville, IN, 46391, USA
| | - Andrew N Miller
- University of Illinois Urbana-Champaign, Illinois Natural History Survey, 1816 South Oak Street, Champaign, IL, 61820-6970, USA
| | - Phillip C Watts
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland.
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199
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O'Neill AM, Worthing KA, Kulkarni N, Li F, Nakatsuji T, McGrosso D, Mills RH, Kalla G, Cheng JY, Norris JM, Pogliano K, Pogliano J, Gonzalez DJ, Gallo RL. Antimicrobials from a feline commensal bacterium inhibit skin infection by drug-resistant S. pseudintermedius. eLife 2021; 10:66793. [PMID: 34664551 PMCID: PMC8592530 DOI: 10.7554/elife.66793] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 10/02/2021] [Indexed: 12/13/2022] Open
Abstract
Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is an important emerging zoonotic pathogen that causes severe skin infections. To combat infections from drug-resistant bacteria, the transplantation of commensal antimicrobial bacteria as a therapeutic has shown clinical promise. We screened a collection of diverse staphylococcus species from domestic dogs and cats for antimicrobial activity against MRSP. A unique strain (S. felis C4) was isolated from feline skin that inhibited MRSP and multiple gram-positive pathogens. Whole genome sequencing and mass spectrometry revealed several secreted antimicrobials including a thiopeptide bacteriocin micrococcin P1 and phenol-soluble modulin beta (PSMβ) peptides that exhibited antimicrobial and anti-inflammatory activity. Fluorescence and electron microscopy revealed that S. felis antimicrobials inhibited translation and disrupted bacterial but not eukaryotic cell membranes. Competition experiments in mice showed that S. felis significantly reduced MRSP skin colonization and an antimicrobial extract from S. felis significantly reduced necrotic skin injury from MRSP infection. These findings indicate a feline commensal bacterium that could be utilized in bacteriotherapy against difficult-to-treat animal and human skin infections.
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Affiliation(s)
- Alan M O'Neill
- Department of Dermatology, University of California, San Diego, San Diego, United States
| | - Kate A Worthing
- College of Veterinary Medicine, University of Arizona, Oro Valley, United States
| | - Nikhil Kulkarni
- Department of Dermatology, University of California, San Diego, San Diego, United States
| | - Fengwu Li
- Department of Dermatology, University of California, San Diego, San Diego, United States
| | - Teruaki Nakatsuji
- Department of Dermatology, University of California, San Diego, San Diego, United States
| | - Dominic McGrosso
- Department of Pharmacology, University of California, San Diego, San Diego, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, United States
| | - Robert H Mills
- Department of Pharmacology, University of California, San Diego, San Diego, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, United States
| | - Gayathri Kalla
- Division of Biological Sciences, University of California, San Diego, San Diego, United States
| | - Joyce Y Cheng
- Department of Dermatology, University of California, San Diego, San Diego, United States
| | - Jacqueline M Norris
- Sydney School of Veterinary Science, University of Sydney, Sydney, Australia
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, San Diego, United States
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, San Diego, United States
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, San Diego, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, United States
| | - Richard L Gallo
- Department of Dermatology, University of California, San Diego, San Diego, United States
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200
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Bishai JD, Palm NW. Small Molecule Metabolites at the Host-Microbiota Interface. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:1725-1733. [PMID: 34544815 PMCID: PMC8500551 DOI: 10.4049/jimmunol.2100528] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/09/2021] [Indexed: 01/15/2023]
Abstract
The trillions of bacteria that constitutively colonize the human gut collectively generate thousands of unique small molecules. These microbial metabolites can accumulate both locally and systemically and potentially influence nearly all aspects of mammalian biology, including immunity, metabolism, and even mood and behavior. In this review, we briefly summarize recent work identifying bioactive microbiota metabolites, the means through which they are synthesized, and their effects on host physiology. Rather than offering an exhaustive list of all known bioactive microbial small molecules, we select a few examples from each key class of metabolites to illustrate the diverse impacts of microbiota-derived compounds on the host. In addition, we attempt to address the microbial logic behind specific biotransformations. Finally, we outline current and emerging strategies for identifying previously undiscovered bioactive microbiota metabolites that may shape human health and disease.
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Affiliation(s)
- Jason D Bishai
- Department of Microbial Pathogenesis, Yale School of Medicine, Yale University, New Haven, CT; and
| | - Noah W Palm
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT
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