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Sengupta S, Pabbaraja S, Mehta G. Natural products from the human microbiome: an emergent frontier in organic synthesis and drug discovery. Org Biomol Chem 2024; 22:4006-4030. [PMID: 38669195 DOI: 10.1039/d4ob00236a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Often referred to as the "second genome", the human microbiome is at the epicenter of complex inter-habitat biochemical networks like the "gut-brain axis", which has emerged as a significant determinant of cognition, overall health and well-being, as well as resistance to antibiotics and susceptibility to diseases. As part of a broader understanding of the nexus between the human microbiome, diseases and microbial interactions, whether encoded secondary metabolites (natural products) play crucial signalling roles has been the subject of intense scrutiny in the recent past. A major focus of these activities involves harvesting the genomic potential of the human microbiome via bioinformatics guided genome mining and culturomics. Through these efforts, an impressive number of structurally intriguing antibiotics, with enhanced chemical diversity vis-à-vis conventional antibiotics have been isolated from human commensal bacteria, thereby generating considerable interest in their total synthesis and expanding their therapeutic space for drug discovery. These developments augur well for the discovery of new drugs and antibiotics, particularly in the context of challenges posed by mycobacterial resistance and emerging new diseases. The current landscape of various synthetic campaigns and drug discovery initiatives on antibacterial natural products from the human microbiome is captured in this review with an intent to stimulate further activities in this interdisciplinary arena among the new generation.
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Affiliation(s)
- Saumitra Sengupta
- School of Chemistry, University of Hyderabad, Hyderabad-500046, India.
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad-500007, India
| | - Srihari Pabbaraja
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad-500007, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Goverdhan Mehta
- School of Chemistry, University of Hyderabad, Hyderabad-500046, India.
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Reuben RC, Torres C. Bacteriocins: potentials and prospects in health and agrifood systems. Arch Microbiol 2024; 206:233. [PMID: 38662051 PMCID: PMC11045635 DOI: 10.1007/s00203-024-03948-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024]
Abstract
Bacteriocins are highly diverse, abundant, and heterogeneous antimicrobial peptides that are ribosomally synthesized by bacteria and archaea. Since their discovery about a century ago, there has been a growing interest in bacteriocin research and applications. This is mainly due to their high antimicrobial properties, narrow or broad spectrum of activity, specificity, low cytotoxicity, and stability. Though initially used to improve food quality and safety, bacteriocins are now globally exploited for innovative applications in human, animal, and food systems as sustainable alternatives to antibiotics. Bacteriocins have the potential to beneficially modulate microbiota, providing viable microbiome-based solutions for the treatment, management, and non-invasive bio-diagnosis of infectious and non-infectious diseases. The use of bacteriocins holds great promise in the modulation of food microbiomes, antimicrobial food packaging, bio-sanitizers and antibiofilm, pre/post-harvest biocontrol, functional food, growth promotion, and sustainable aquaculture. This can undoubtedly improve food security, safety, and quality globally. This review highlights the current trends in bacteriocin research, especially the increasing research outputs and funding, which we believe may proportionate the soaring global interest in bacteriocins. The use of cutting-edge technologies, such as bioengineering, can further enhance the exploitation of bacteriocins for innovative applications in human, animal, and food systems.
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Affiliation(s)
- Rine Christopher Reuben
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain.
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain
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Nicholas-Haizelden K, Murphy B, Hoptroff M, Horsburgh MJ. Bioprospecting the Skin Microbiome: Advances in Therapeutics and Personal Care Products. Microorganisms 2023; 11:1899. [PMID: 37630459 PMCID: PMC10456854 DOI: 10.3390/microorganisms11081899] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Bioprospecting is the discovery and exploration of biological diversity found within organisms, genetic elements or produced compounds with prospective commercial or therapeutic applications. The human skin is an ecological niche which harbours a rich and compositional diversity microbiome stemming from the multifactorial interactions between the host and microbiota facilitated by exploitable effector compounds. Advances in the understanding of microbial colonisation mechanisms alongside species and strain interactions have revealed a novel chemical and biological understanding which displays applicative potential. Studies elucidating the organismal interfaces and concomitant understanding of the central processes of skin biology have begun to unravel a potential wealth of molecules which can exploited for their proposed functions. A variety of skin-microbiome-derived compounds display prospective therapeutic applications, ranging from antioncogenic agents relevant in skin cancer therapy to treatment strategies for antimicrobial-resistant bacterial and fungal infections. Considerable opportunities have emerged for the translation to personal care products, such as topical agents to mitigate various skin conditions such as acne and eczema. Adjacent compound developments have focused on cosmetic applications such as reducing skin ageing and its associated changes to skin properties and the microbiome. The skin microbiome contains a wealth of prospective compounds with therapeutic and commercial applications; however, considerable work is required for the translation of in vitro findings to relevant in vivo models to ensure translatability.
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Affiliation(s)
- Keir Nicholas-Haizelden
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, UK;
| | - Barry Murphy
- Unilever Research & Development, Port Sunlight, Wirral CH63 3JW, UK; (B.M.); (M.H.)
| | - Michael Hoptroff
- Unilever Research & Development, Port Sunlight, Wirral CH63 3JW, UK; (B.M.); (M.H.)
| | - Malcolm J. Horsburgh
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, UK;
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Del Rio Flores A, Narayanamoorthy M, Cai W, Zhai R, Yang S, Shen Y, Seshadri K, De Matias K, Xue Z, Zhang W. Biosynthesis of Isonitrile Lipopeptide Metallophores from Pathogenic Mycobacteria. Biochemistry 2023; 62:824-834. [PMID: 36638317 PMCID: PMC9905339 DOI: 10.1021/acs.biochem.2c00611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Isonitrile lipopeptides (INLPs) are known to be related to the virulence of pathogenic mycobacteria by mediating metal transport, but their biosynthesis remains obscure. In this work, we use in vitro biochemical assays, site-directed mutagenesis, chemical synthesis, and spectroscopy techniques to scrutinize the activity of core enzymes required for INLP biosynthesis in mycobacteria. Compared to environmental Streptomyces, pathogenic Mycobacterium employ a similar chemical logic and enzymatic machinery in INLP biosynthesis, differing mainly in the fatty-acyl chain length, which is controlled by multiple enzymes in the pathway. Our in-depth study on the non-heme iron(II) and α-ketoglutarate-dependent dioxygenase for isonitrile generation, including Rv0097 from Mycobacterium tuberculosis (Mtb), demonstrates that it recognizes a free-standing small molecule substrate, different from the recent hypothesis that a carrier protein is required for Rv0097 in Mtb. A key residue in Rv0097 is further identified to dictate the varied fatty-acyl chain length specificity between Streptomyces and Mycobacterium.
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Affiliation(s)
- Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Maanasa Narayanamoorthy
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Wenlong Cai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Rui Zhai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Siyue Yang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Yuanbo Shen
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Kaushik Seshadri
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Kyle De Matias
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Zhaoqiang Xue
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
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Saroha T, Sharma S, Choksket S, Korpole S, Patil PB. Limosilactobacillus walteri sp. nov., a novel probiotic antimicrobial lipopeptide-producing bacterium. FEMS Microbiol Lett 2023; 370:6988174. [PMID: 36646427 DOI: 10.1093/femsle/fnad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/06/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
A Gram-positive facultative anaerobe, nonspore forming, and nonmotile bacterial strain M31 was isolated from faecal contaminated soil. The strain is previously reported to produce a novel antimicrobial lipopeptide and displayed probiotic properties. The strain M31 is catalase negative and fermented d-galactose, d-glucose, esculin, d-maltose, d-lactose, d-melibiose, d-raffinose, d-saccharose (weak reaction), d-xylose (weak reaction), d-ribose (weak reaction), and l-arabinose (weak reaction). The majority of fatty acids were C16:0 (53.9%), C18:0 (26.9%), and C19:0 cyclo ω8c (19.1%). The genome is 2 234 040 bp long with 38.81% guanine-cytosine (GC) content. The pairwise ortho average nucleotide identity and digital DNA-DNA hybridization values of strain M31 with its closest relative species from Limosilactobacillus reuteri clade and Lm. rudii is below the recommended cut-off of 95% and 70%, respectively. Herein, we propose Lm. walteri sp. nov. as a novel species of the genus Limosilactobacillus with M31 = MTCC 12838 = JCM 32759 = KCTC 25569.
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Affiliation(s)
- Tanu Saroha
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shikha Sharma
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Stanzin Choksket
- Microbial Type Culture Collection and Gene Bank Division, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Suresh Korpole
- Microbial Type Culture Collection and Gene Bank Division, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
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Nguyen UT, Kalan LR. Forgotten fungi: the importance of the skin mycobiome. Curr Opin Microbiol 2022; 70:102235. [PMID: 36372041 PMCID: PMC10044452 DOI: 10.1016/j.mib.2022.102235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/21/2022] [Accepted: 10/19/2022] [Indexed: 11/13/2022]
Abstract
The mosaic ecosystems of microbes that live on our skin encompass not only bacteria but also fungi, microeukaryotes, and viruses. As the second most prevalent group, unique fungal communities are found across the dry, moist, and oily microenvironments of human skin, and alterations of these communities are largely driven by changes in skin physiology throughout an individual's lifespan. Fungi have also been associated with infection and dermatological disorders, resulting from the disrupted balance between fungal-bacterial networks on the skin. Mechanisms of colonization resistance toward fungi in the skin microbiome of animals have advanced our understanding in conservation strategies, yet in the human skin, the fungal microbiome (mycobiome) remains vastly unexplored. Here, we review recent studies on the role of fungi in the skin microbiome, emphasizing how fungal-bacterial interactions at the skin surface play an important ecological function in vertebrate hosts.
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Affiliation(s)
- Uyen Thy Nguyen
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, United States; Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States.
| | - Lindsay R Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States; Department of Medicine, Division of Infectious Disease, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States.
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Liao G, Tang X. Mining the Microbial Chemistry behind Tooth Decay. Biochemistry 2021; 61:2779-2781. [PMID: 34813289 DOI: 10.1021/acs.biochem.1c00652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ge Liao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.,Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Xiaoyu Tang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
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Shen B, Tang Y, Baltz RH, Gonzalez R. Introduction to the special issue: "Natural Product Discovery and Development in the Genomic Era: 2021". J Ind Microbiol Biotechnol 2021; 48:6255434. [PMID: 33904896 PMCID: PMC9113160 DOI: 10.1093/jimb/kuab030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 11/14/2022]
Affiliation(s)
- Ben Shen
- Departments of Chemistry and Molecular Medicine, and Natural Products Discovery Center at Scripps Research, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Yi Tang
- Departments of Chemistry and Biochemistry, and Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
| | - Richard H Baltz
- CognoGen Biotechnology Consulting, 7757 Uliva Way, Sarasota, FL 34238, USA
| | - Ramon Gonzalez
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL 33620, USA
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