1
|
Que M, Li S, Xia Q, Li X, Luo X, Zhan G, Luo A. Microbiota-gut-brain axis in perioperative neurocognitive and depressive disorders: Pathogenesis to treatment. Neurobiol Dis 2024; 200:106627. [PMID: 39111702 DOI: 10.1016/j.nbd.2024.106627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 08/28/2024] Open
Abstract
An increasing number of people undergo anesthesia and surgery. Perioperative neurocognitive and depressive disorders are common central nervous system complications with similar pathogeneses. These conditions pose a deleterious threat to human health and a significant societal burden. In recent years, numerous studies have focused on the role of the gut microbiota and its metabolites in the central nervous system via the gut-brain axis. Its involvement in perioperative neurocognitive and depressive disorders has attracted considerable attention. This review aimed to elucidate the role of the gut microbiota and its metabolites in the pathogenesis of perioperative neurocognitive and depressive disorders, as well as the value of targeted interventions and treatments.
Collapse
Affiliation(s)
- Mengxin Que
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health; Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shiyong Li
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health; Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qian Xia
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health; Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xing Li
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health; Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoxiao Luo
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Gaofeng Zhan
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health; Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Ailin Luo
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health; Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| |
Collapse
|
2
|
Schmartz GP, Rehner J, Gund MP, Keller V, Molano LAG, Rupf S, Hannig M, Berger T, Flockerzi E, Seitz B, Fleser S, Schmitt-Grohé S, Kalefack S, Zemlin M, Kunz M, Götzinger F, Gevaerd C, Vogt T, Reichrath J, Diehl L, Hecksteden A, Meyer T, Herr C, Gurevich A, Krug D, Hegemann J, Bozhueyuek K, Gulder TAM, Fu C, Beemelmanns C, Schattenberg JM, Kalinina OV, Becker A, Unger M, Ludwig N, Seibert M, Stein ML, Hanna NL, Martin MC, Mahfoud F, Krawczyk M, Becker SL, Müller R, Bals R, Keller A. Decoding the diagnostic and therapeutic potential of microbiota using pan-body pan-disease microbiomics. Nat Commun 2024; 15:8261. [PMID: 39327438 PMCID: PMC11427559 DOI: 10.1038/s41467-024-52598-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 09/13/2024] [Indexed: 09/28/2024] Open
Abstract
The human microbiome emerges as a promising reservoir for diagnostic markers and therapeutics. Since host-associated microbiomes at various body sites differ and diseases do not occur in isolation, a comprehensive analysis strategy highlighting the full potential of microbiomes should include diverse specimen types and various diseases. To ensure robust data quality and comparability across specimen types and diseases, we employ standardized protocols to generate sequencing data from 1931 prospectively collected specimens, including from saliva, plaque, skin, throat, eye, and stool, with an average sequencing depth of 5.3 gigabases. Collected from 515 patients, these samples yield an average of 3.7 metagenomes per patient. Our results suggest significant microbial variations across diseases and specimen types, including unexpected anatomical sites. We identify 583 unexplored species-level genome bins (SGBs) of which 189 are significantly disease-associated. Of note, the existence of microbial resistance genes in one specimen was indicative of the same resistance genes in other specimens of the same patient. Annotated and previously undescribed SGBs collectively harbor 28,315 potential biosynthetic gene clusters (BGCs), with 1050 significant correlations to diseases. Our combinatorial approach identifies distinct SGBs and BGCs, emphasizing the value of pan-body pan-disease microbiomics as a source for diagnostic and therapeutic strategies.
Collapse
Affiliation(s)
- Georges P Schmartz
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Jacqueline Rehner
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421, Homburg, Germany
| | - Madline P Gund
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, 66421, Homburg, Germany
| | - Verena Keller
- Department of Medicine II, Saarland University Medical Center, 66421, Homburg, Germany
| | | | - Stefan Rupf
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, 66421, Homburg, Germany
- Synoptic Dentistry, Saarland University, 66421, Homburg, Germany
| | - Matthias Hannig
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, 66421, Homburg, Germany
| | - Tim Berger
- Department of Ophthalmology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Elias Flockerzi
- Department of Ophthalmology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Berthold Seitz
- Department of Ophthalmology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Sara Fleser
- Department of General Pediatrics and Neonatology, Saarland University, 66421, Homburg, Germany
| | - Sabina Schmitt-Grohé
- Department of General Pediatrics and Neonatology, Saarland University, 66421, Homburg, Germany
| | - Sandra Kalefack
- Department of General Pediatrics and Neonatology, Saarland University, 66421, Homburg, Germany
| | - Michael Zemlin
- Department of General Pediatrics and Neonatology, Saarland University, 66421, Homburg, Germany
| | - Michael Kunz
- Department of Internal Medicine III, Cardiology, Angiology, Intensive Care Medicine, Saarland University Hospital, 66421, Homburg, Germany
| | - Felix Götzinger
- Department of Internal Medicine III, Cardiology, Angiology, Intensive Care Medicine, Saarland University Hospital, 66421, Homburg, Germany
| | - Caroline Gevaerd
- Clinic for Dermatology, Venereology, and Allergology, 66421, Homburg, Germany
| | - Thomas Vogt
- Clinic for Dermatology, Venereology, and Allergology, 66421, Homburg, Germany
| | - Jörg Reichrath
- Clinic for Dermatology, Venereology, and Allergology, 66421, Homburg, Germany
| | - Lisa Diehl
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Anne Hecksteden
- Institute for Sport and Preventive Medicine, Saarland University, 66123, Saarbrücken, Germany
- Chair of Sports Medicine, Institute of Physiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Tim Meyer
- Institute for Sport and Preventive Medicine, Saarland University, 66123, Saarbrücken, Germany
| | - Christian Herr
- Department of Internal Medicine V - Pulmonology, Allergology, Intensive Care Medicine, Saarland University, Saarbrücken, Germany
| | - Alexey Gurevich
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
- Center for Bioinformatics Saar and Saarland University, Saarland Informatics Campus, 66123, Saarbrücken, Germany
| | - Daniel Krug
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
| | - Julian Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
| | - Kenan Bozhueyuek
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
| | - Tobias A M Gulder
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
| | - Chengzhang Fu
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
| | - Christine Beemelmanns
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
| | - Jörn M Schattenberg
- Department of Medicine II, Saarland University Medical Center, 66421, Homburg, Germany
| | - Olga V Kalinina
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
| | - Anouck Becker
- Department for Neurology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Marcus Unger
- Department for Neurology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Nicole Ludwig
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Martina Seibert
- Department of Ophthalmology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Marie-Louise Stein
- Department of Ophthalmology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Nikolas Loka Hanna
- Department of Internal Medicine V - Pulmonology, Allergology, Intensive Care Medicine, Saarland University, Saarbrücken, Germany
| | - Marie-Christin Martin
- Department of Ophthalmology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Felix Mahfoud
- Department of Internal Medicine III, Cardiology, Angiology, Intensive Care Medicine, Saarland University Hospital, 66421, Homburg, Germany
| | - Marcin Krawczyk
- Department of Medicine II, Saarland University Medical Center, 66421, Homburg, Germany
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421, Homburg, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
- PharmaScienceHub, 66123, Saarbrücken, Germany
| | - Robert Bals
- Department of Internal Medicine V - Pulmonology, Allergology, Intensive Care Medicine, Saarland University, Saarbrücken, Germany
- PharmaScienceHub, 66123, Saarbrücken, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany.
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany.
- PharmaScienceHub, 66123, Saarbrücken, Germany.
| |
Collapse
|
3
|
Schmartz GP, Rehner J, Schuff MJ, Molano LAG, Becker SL, Krawczyk M, Tagirdzhanov A, Gurevich A, Francke R, Müller R, Keller V, Keller A. Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes. Nat Commun 2024; 15:8263. [PMID: 39327429 PMCID: PMC11427580 DOI: 10.1038/s41467-024-52669-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 09/13/2024] [Indexed: 09/28/2024] Open
Abstract
Understanding human, animal, and environmental microbiota is essential for advancing global health and combating antimicrobial resistance (AMR). We investigate the oral and gut microbiota of 48 animal species in captivity, comparing them to those of wildlife animals. Specifically, we characterize the microbiota composition, metabolic pathways, AMR genes, and biosynthetic gene clusters (BGCs) encoding the production of specialized metabolites. Our results reveal a high diversity of microbiota, with 585 novel species-level genome bins (SGBs) and 484 complete BGCs identified. Functional gene analysis of microbiomes shows diet-dependent variations. Furthermore, by comparing our findings to wildlife-derived microbiomes, we observe the impact of captivity on the animal microbiome, including examples of converging microbiome compositions. Importantly, our study identifies AMR genes against commonly used veterinary antibiotics, as well as resistance to vancomycin, a critical antibiotic in human medicine. These findings underscore the importance of the 'One Health' approach and the potential for zoonotic transmission of pathogenic bacteria and AMR. Overall, our study contributes to a better understanding of the complexity of the animal microbiome and highlights its BGC diversity relevant to the discovery of novel antimicrobial compounds.
Collapse
Affiliation(s)
- Georges P Schmartz
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Jacqueline Rehner
- Institute of Medical Microbiology and Hygiene, 66421 Saarland University, Homburg, Germany
| | - Miriam J Schuff
- Institute of Medical Microbiology and Hygiene, 66421 Saarland University, Homburg, Germany
| | | | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, 66421 Saarland University, Homburg, Germany
| | - Marcin Krawczyk
- Department of Medicine II, 66421 Saarland University, Homburg, Germany
| | - Azat Tagirdzhanov
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, 66123, Saarbrücken, Germany
| | - Alexey Gurevich
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, 66123, Saarbrücken, Germany
- Department of Computer Science, Saarland University, 66123, Saarbrücken, Germany
| | | | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, 66123, Saarbrücken, Germany
| | - Verena Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany.
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, 66123, Saarbrücken, Germany.
| |
Collapse
|
4
|
Wang Y, Shi YN, Xiang H, Shi YM. Exploring nature's battlefield: organismic interactions in the discovery of bioactive natural products. Nat Prod Rep 2024. [PMID: 39316448 DOI: 10.1039/d4np00018h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
Covering: up to March 2024.Microbial natural products have historically been a cornerstone for the discovery of therapeutic agents. Advanced (meta)genome sequencing technologies have revealed that microbes harbor far greater biosynthetic capabilities than previously anticipated. However, despite the application of CRISPR/Cas-based gene editing and high-throughput technologies to activate silent biosynthetic gene clusters, the rapid identification of new natural products has not led to a proportional increase in the discovery rate of lead compounds or drugs. A crucial issue in this gap may be insufficient knowledge about the inherent biological and physiological functions of microbial natural products. Addressing this gap necessitates recognizing that the generation of functional natural products is deeply rooted in the interactions between the producing microbes and other (micro)organisms within their ecological contexts, an understanding that is essential for harnessing their potential therapeutic benefits. In this review, we highlight the discovery of functional microbial natural products from diverse niches, including those associated with humans, nematodes, insects, fungi, protozoa, plants, and marine animals. Many of these findings result from an organismic-interaction-guided strategy using multi-omic approaches. The current importance of this topic lies in its potential to advance drug discovery in an era marked by increasing antimicrobial resistance.
Collapse
Affiliation(s)
- Yuyang Wang
- Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Yan-Ni Shi
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Hao Xiang
- Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Ming Shi
- Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
5
|
Baindara P, Dinata R, Mandal SM. Marine Bacteriocins: An Evolutionary Gold Mine to Payoff Antibiotic Resistance. Mar Drugs 2024; 22:388. [PMID: 39330269 PMCID: PMC11433236 DOI: 10.3390/md22090388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2024] [Revised: 08/25/2024] [Accepted: 08/26/2024] [Indexed: 09/28/2024] Open
Abstract
The rapid evolution of drug resistance is one of the greatest health issues of the 21st century. There is an alarming situation to find new therapeutic strategies or candidate drugs to tackle ongoing multi-drug resistance development. The marine environment is one of the prime natural ecosystems on Earth, the majority of which is still unexplored, especially when it comes to the microbes. A wide variety of bioactive compounds have been obtained from a varied range of marine organisms; however, marine bacteria-produced bacteriocins are still undermined. Owing to the distinct environmental stresses that marine bacterial communities encounter, their bioactive compounds frequently undergo distinct adaptations that confer on them a variety of shapes and functions, setting them apart from their terrestrial counterparts. Bacterially produced ribosomally synthesized and posttranslationally modified peptides (RiPPs), known as bacteriocins, are one of the special interests to be considered as an alternative to conventional antibiotics because of their variety in structure and diverse potential biological activities. Additionally, the gut microbiome of marine creatures are a largely unexplored source of new bacteriocins with promising activities. There is a huge possibility of novel bacteriocins from marine bacterial communities that might come out as efficient candidates to fight against antibiotic resistance, especially in light of the growing pressure from antibiotic-resistant diseases and industrial desire for innovative treatments. The present review summarizes known and fully characterized marine bacteriocins, their evolutionary aspects, challenges, and the huge possibilities of unexplored novel bacteriocins from marine bacterial communities present in diverse marine ecosystems.
Collapse
Affiliation(s)
- Piyush Baindara
- Animal Sciences Research Center, Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Roy Dinata
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata 741246, India;
| | - Santi M. Mandal
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA;
| |
Collapse
|
6
|
Chen J, Wang W, Hu X, Yue Y, Lu X, Wang C, Wei B, Zhang H, Wang H. Medium-sized peptides from microbial sources with potential for antibacterial drug development. Nat Prod Rep 2024; 41:1235-1263. [PMID: 38651516 DOI: 10.1039/d4np00002a] [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: 04/25/2024]
Abstract
Covering: 1993 to the end of 2022As the rapid development of antibiotic resistance shrinks the number of clinically available antibiotics, there is an urgent need for novel options to fill the existing antibiotic pipeline. In recent years, antimicrobial peptides have attracted increased interest due to their impressive broad-spectrum antimicrobial activity and low probability of antibiotic resistance. However, macromolecular antimicrobial peptides of plant and animal origin face obstacles in antibiotic development because of their extremely short elimination half-life and poor chemical stability. Herein, we focus on medium-sized antibacterial peptides (MAPs) of microbial origin with molecular weights below 2000 Da. The low molecular weight is not sufficient to form complex protein conformations and is also associated to a better chemical stability and easier modifications. Microbially-produced peptides are often composed of a variety of non-protein amino acids and terminal modifications, which contribute to improving the elimination half-life of compounds. Therefore, MAPs have great potential for drug discovery and are likely to become key players in the development of next-generation antibiotics. In this review, we provide a detailed exploration of the modes of action demonstrated by 45 MAPs and offer a concise summary of the structure-activity relationships observed in these MAPs.
Collapse
Affiliation(s)
- Jianwei Chen
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xubin Hu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yujie Yue
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xingyue Lu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chenjie Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Bin Wei
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Huawei Zhang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| |
Collapse
|
7
|
Siddiqui SZ, Saleha Z, Nayak A. Identification of clusters of secondary metabolite biosynthetic genes in the Camelina sativa genome. Nat Prod Res 2024:1-7. [PMID: 39101233 DOI: 10.1080/14786419.2024.2385695] [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: 02/18/2024] [Revised: 06/19/2024] [Accepted: 07/21/2024] [Indexed: 08/06/2024]
Abstract
Multidrug-resistant pathogens pose an earnest risk to human health. Therefore, new antibiotics need to be developed quickly. Most of the antibiotics we use today are derived from secondary metabolites, which are produced by plants. Genome mining tools allow us to detect biosynthetic gene clusters (BGCs) responsible for the production of secondary metabolites. Focusing on the most promising BGCs-coding antibiotics with unique pathways is currently a challenge. In silico approach like genome mining are used to visualise the action of these bioactive chemicals. Camelina sativa is a well-known medicinal plant and it would be interesting to study its secondary metabolites. In this work, we found seven bioactive compounds in this plant using the genome mining approach. Further, the clusters of genes involved in the biosynthesis of these compounds were analysed with their metabolic pathways. This work illuminates new ground on the evolution of BGCs for the nutritional improvement of C. sativa.
Collapse
Affiliation(s)
- Shagufi Zea Siddiqui
- Department of Life Science, Guru Nanak Institute of Pharmaceutical Science and Technology, Kolkata, India
| | - Zaryab Saleha
- Department of Life Science, Guru Nanak Institute of Pharmaceutical Science and Technology, Kolkata, India
| | - Aditi Nayak
- Department of Life Science, Guru Nanak Institute of Pharmaceutical Science and Technology, Kolkata, India
| |
Collapse
|
8
|
Li Q, Feng H, Tian Q, Xiang Y, Wang X, He YX, Zhu K. Discovery of antibacterial diketones against gram-positive bacteria. Cell Chem Biol 2024:S2451-9456(24)00277-0. [PMID: 39089260 DOI: 10.1016/j.chembiol.2024.06.017] [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: 10/23/2023] [Revised: 04/21/2024] [Accepted: 06/28/2024] [Indexed: 08/03/2024]
Abstract
The rapid rise of antibiotic resistance calls for the discovery of new antibiotics with distinct antibacterial mechanisms. New target mining is indispensable for developing antibiotics. Plant-microbial antibiotics are appealing to underexplored sources due to a dearth of comprehensive understanding of antibacterial activity and the excavation of new targets. Here, a series of phloroglucinol derivatives of plant-root-associated Pseudomonas fluorescens were synthesized for structure-activity relationship analysis. Notably, 2,4-diproylphloroglucinol (DPPG) displayed efficient bactericidal activity against a wide range of gram-positive bacteria. Importantly, mechanistic study exhibits that DPPG binds to type II NADH dehydrogenase (NDH-2), an essential enzyme catalyzing the transfer of electrons from NADH to quinones in the electron transport chain (ETC), blocking electron transfer in S. aureus. Last, we validated the efficacy of DPPG in vivo through animal infection models. Our findings not only provide a distinct antibiotic lead to treat multidrug resistant pathogens but also identify a promising antibacterial target.
Collapse
Affiliation(s)
- Qian Li
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Hanzhong Feng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Qiong Tian
- State Key Laboratory of Applied Organic Chemistry, Department of Chemistry and School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Yun Xiang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiaolei Wang
- State Key Laboratory of Applied Organic Chemistry, Department of Chemistry and School of Pharmacy, Lanzhou University, Lanzhou 730000, China.
| | - Yong-Xing He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China.
| | - Kui Zhu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
9
|
Semmler F, Regis Belisário-Ferrari M, Kulosa M, Kaysser L. The Metabolic Potential of the Human Lung Microbiome. Microorganisms 2024; 12:1448. [PMID: 39065215 PMCID: PMC11278768 DOI: 10.3390/microorganisms12071448] [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: 06/20/2024] [Revised: 07/05/2024] [Accepted: 07/13/2024] [Indexed: 07/28/2024] Open
Abstract
The human lung microbiome remains largely underexplored, despite its potential implications in the pharmacokinetics of inhaled drugs and its involvement in lung diseases. Interactions within these bacterial communities and with the host are complex processes which often involve microbial small molecules. In this study, we employed a computational approach to describe the metabolic potential of the human lung microbiome. By utilizing antiSMASH and BiG-SCAPE software, we identified 1831 biosynthetic gene clusters for the production of specialized metabolites in a carefully compiled genome database of lung-associated bacteria and fungi. It was shown that RiPPs represent the largest class of natural products within the bacteriome, while NRPs constitute the largest class of natural products in the lung mycobiome. All predicted BGCs were further categorized into 767 gene cluster families, and a subsequent network analysis highlighted that these families are widely distributed and contain many uncharacterized members. Moreover, in-depth annotation allowed the assignment of certain gene clusters to putative lung-specific functions within the microbiome, such as osmoadaptation or surfactant synthesis. This study establishes the lung microbiome as a prolific source for secondary metabolites and lays the groundwork for detailed investigation of this unique environment.
Collapse
Affiliation(s)
| | | | | | - Leonard Kaysser
- Department of Pharmaceutical Biology, Institute for Drug Discovery, University of Leipzig, 04317 Leipzig, Germany; (F.S.); (M.R.B.-F.); (M.K.)
| |
Collapse
|
10
|
Lee H, Yang X, Jin PR, Won KJ, Kim CH, Jeong H. The Discovery of Gut Microbial Metabolites as Modulators of Host Susceptibility to Acetaminophen-Induced Hepatotoxicity. Drug Metab Dispos 2024; 52:754-764. [PMID: 38302428 PMCID: PMC11257691 DOI: 10.1124/dmd.123.001541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/11/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024] Open
Abstract
The mammalian gut microbiota plays diverse and essential roles in modulating host physiology. Key mediators determining the outcome of the microbiota-host interactions are the small molecule metabolites produced by the gut microbiota. The liver is a major organ exposed to gut microbial metabolites, and it serves as the nexus for maintaining healthy interactions between the gut microbiota and the host. At the same time, the liver is the primary target of potentially harmful gut microbial metabolites. In this review, we provide an up-to-date list of gut microbial metabolites that have been identified to either increase or decrease host susceptibility to acetaminophen (APAP)-induced liver injury. The signaling pathways and molecular factors involved in the progression of APAP-induced hepatotoxicity are well-established, and we propose that the mouse model of APAP-induced hepatotoxicity serves as a model system for uncovering gut microbial metabolites with previously unknown functions. Furthermore, we envision that gut microbial metabolites identified to alter APAP-induced hepatotoxicity likely have broader implications in other liver diseases. SIGNIFICANCE STATEMENT: This review provides an overview of the role of the gut microbiota in modulating the host susceptibility to acetaminophen (APAP)-induced liver injury. It focuses on the roles of gut bacterial small molecule metabolites as mediators of the interaction between the gut microbiota and the liver. It also illustrates the utility of APAP-induced liver injury as a model to identify gut microbial metabolites with biological function.
Collapse
Affiliation(s)
- Hyunwoo Lee
- Department of Industrial and Molecular Pharmaceutics (H.L., X.Y., P.-R.J., K.-J.W., H.J.), Department of Pharmacy Practice (H.J.), and College of Pharmacy, and Department of Comparative Pathobiology, College of Veterinary Medicine (H.L.), Purdue University, West Lafayette, Indiana and Department of Pathology and Mary H. Weiser Food Allergy Center and Rogel Center for Cancer Research, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.)
| | - Xiaotong Yang
- Department of Industrial and Molecular Pharmaceutics (H.L., X.Y., P.-R.J., K.-J.W., H.J.), Department of Pharmacy Practice (H.J.), and College of Pharmacy, and Department of Comparative Pathobiology, College of Veterinary Medicine (H.L.), Purdue University, West Lafayette, Indiana and Department of Pathology and Mary H. Weiser Food Allergy Center and Rogel Center for Cancer Research, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.)
| | - Pei-Ru Jin
- Department of Industrial and Molecular Pharmaceutics (H.L., X.Y., P.-R.J., K.-J.W., H.J.), Department of Pharmacy Practice (H.J.), and College of Pharmacy, and Department of Comparative Pathobiology, College of Veterinary Medicine (H.L.), Purdue University, West Lafayette, Indiana and Department of Pathology and Mary H. Weiser Food Allergy Center and Rogel Center for Cancer Research, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.)
| | - Kyoung-Jae Won
- Department of Industrial and Molecular Pharmaceutics (H.L., X.Y., P.-R.J., K.-J.W., H.J.), Department of Pharmacy Practice (H.J.), and College of Pharmacy, and Department of Comparative Pathobiology, College of Veterinary Medicine (H.L.), Purdue University, West Lafayette, Indiana and Department of Pathology and Mary H. Weiser Food Allergy Center and Rogel Center for Cancer Research, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.)
| | - Chang H Kim
- Department of Industrial and Molecular Pharmaceutics (H.L., X.Y., P.-R.J., K.-J.W., H.J.), Department of Pharmacy Practice (H.J.), and College of Pharmacy, and Department of Comparative Pathobiology, College of Veterinary Medicine (H.L.), Purdue University, West Lafayette, Indiana and Department of Pathology and Mary H. Weiser Food Allergy Center and Rogel Center for Cancer Research, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.)
| | - Hyunyoung Jeong
- Department of Industrial and Molecular Pharmaceutics (H.L., X.Y., P.-R.J., K.-J.W., H.J.), Department of Pharmacy Practice (H.J.), and College of Pharmacy, and Department of Comparative Pathobiology, College of Veterinary Medicine (H.L.), Purdue University, West Lafayette, Indiana and Department of Pathology and Mary H. Weiser Food Allergy Center and Rogel Center for Cancer Research, University of Michigan School of Medicine, Ann Arbor, Michigan (C.H.K.)
| |
Collapse
|
11
|
Santos-Júnior CD, Torres MDT, Duan Y, Rodríguez Del Río Á, Schmidt TSB, Chong H, Fullam A, Kuhn M, Zhu C, Houseman A, Somborski J, Vines A, Zhao XM, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP. Discovery of antimicrobial peptides in the global microbiome with machine learning. Cell 2024; 187:3761-3778.e16. [PMID: 38843834 DOI: 10.1016/j.cell.2024.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 04/11/2024] [Accepted: 05/06/2024] [Indexed: 06/25/2024]
Abstract
Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a machine-learning-based approach to predict antimicrobial peptides (AMPs) within the global microbiome and leverage a vast dataset of 63,410 metagenomes and 87,920 prokaryotic genomes from environmental and host-associated habitats to create the AMPSphere, a comprehensive catalog comprising 863,498 non-redundant peptides, few of which match existing databases. AMPSphere provides insights into the evolutionary origins of peptides, including by duplication or gene truncation of longer sequences, and we observed that AMP production varies by habitat. To validate our predictions, we synthesized and tested 100 AMPs against clinically relevant drug-resistant pathogens and human gut commensals both in vitro and in vivo. A total of 79 peptides were active, with 63 targeting pathogens. These active AMPs exhibited antibacterial activity by disrupting bacterial membranes. In conclusion, our approach identified nearly one million prokaryotic AMP sequences, an open-access resource for antibiotic discovery.
Collapse
Affiliation(s)
- Célio Dias Santos-Júnior
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China; Laboratory of Microbial Processes & Biodiversity - LMPB, Department of Hydrobiology, Universidade Federal de São Carlos - UFSCar, São Carlos, São Paulo 13565-905, Brazil
| | - Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA; Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Yiqian Duan
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China
| | - Álvaro Rodríguez Del Río
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Thomas S B Schmidt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; APC Microbiome & School of Medicine, University College Cork, Cork, Ireland
| | - Hui Chong
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China
| | - Anthony Fullam
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael Kuhn
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Chengkai Zhu
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China
| | - Amy Houseman
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China
| | - Jelena Somborski
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China
| | - Anna Vines
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China; Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China; State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Max Delbrück Centre for Molecular Medicine, Berlin, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA; Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA.
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China; Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba, QLD, Australia.
| |
Collapse
|
12
|
Qadri H, Shah AH, Almilaibary A, Mir MA. Microbiota, natural products, and human health: exploring interactions for therapeutic insights. Front Cell Infect Microbiol 2024; 14:1371312. [PMID: 39035357 PMCID: PMC11257994 DOI: 10.3389/fcimb.2024.1371312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 06/03/2024] [Indexed: 07/23/2024] Open
Abstract
The symbiotic relationship between the human digestive system and its intricate microbiota is a captivating field of study that continues to unfold. Comprising predominantly anaerobic bacteria, this complex microbial ecosystem, teeming with trillions of organisms, plays a crucial role in various physiological processes. Beyond its primary function in breaking down indigestible dietary components, this microbial community significantly influences immune system modulation, central nervous system function, and disease prevention. Despite the strides made in microbiome research, the precise mechanisms underlying how bacterial effector functions impact mammalian and microbiome physiology remain elusive. Unlike the traditional DNA-RNA-protein paradigm, bacteria often communicate through small molecules, underscoring the imperative to identify compounds produced by human-associated bacteria. The gut microbiome emerges as a linchpin in the transformation of natural products, generating metabolites with distinct physiological functions. Unraveling these microbial transformations holds the key to understanding the pharmacological activities and metabolic mechanisms of natural products. Notably, the potential to leverage gut microorganisms for large-scale synthesis of bioactive compounds remains an underexplored frontier with promising implications. This review serves as a synthesis of current knowledge, shedding light on the dynamic interplay between natural products, bacteria, and human health. In doing so, it contributes to our evolving comprehension of microbiome dynamics, opening avenues for innovative applications in medicine and therapeutics. As we delve deeper into this intricate web of interactions, the prospect of harnessing the power of the gut microbiome for transformative medical interventions becomes increasingly tantalizing.
Collapse
Affiliation(s)
- Hafsa Qadri
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Abdul Haseeb Shah
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Abdullah Almilaibary
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
- Department of Family and Community Medicine, Faculty of Medicine, Al Baha University, Al Bahah, Saudi Arabia
| | - Manzoor Ahmad Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
| |
Collapse
|
13
|
Sanford PA, Blaby I, Yoshikuni Y, Woolston BM. An efficient cre-based workflow for genomic integration and expression of large biosynthetic pathways in Eubacterium limosum. Biotechnol Bioeng 2024. [PMID: 38956879 DOI: 10.1002/bit.28796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/20/2024] [Accepted: 06/16/2024] [Indexed: 07/04/2024]
Abstract
Acetogenic Clostridia are obligate anaerobes that have emerged as promising microbes for the renewable production of biochemicals owing to their ability to efficiently metabolize sustainable single-carbon feedstocks. Additionally, Clostridia are increasingly recognized for their biosynthetic potential, with recent discoveries of diverse secondary metabolites ranging from antibiotics to pigments to modulators of the human gut microbiota. Lack of efficient methods for genomic integration and expression of large heterologous DNA constructs remains a major challenge in studying biosynthesis in Clostridia and using them for metabolic engineering applications. To overcome this problem, we harnessed chassis-independent recombinase-assisted genome engineering (CRAGE) to develop a workflow for facile integration of large gene clusters (>10 kb) into the human gut acetogen Eubacterium limosum. We then integrated a non-ribosomal peptide synthetase gene cluster from the gut anaerobe Clostridium leptum, which previously produced no detectable product in traditional heterologous hosts. Chromosomal expression in E. limosum without further optimization led to production of phevalin at 2.4 mg/L. These results further expand the molecular toolkit for a highly tractable member of the Clostridia, paving the way for sophisticated pathway engineering efforts, and highlighting the potential of E. limosum as a Clostridial chassis for exploration of anaerobic natural product biosynthesis.
Collapse
Affiliation(s)
- Patrick A Sanford
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts, USA
| | - Ian Blaby
- Joint Genome Institute, Lawrence Berkeley National Laboratory, The US Department of Energy, Berkeley, California, USA
| | - Yasuo Yoshikuni
- Joint Genome Institute, Lawrence Berkeley National Laboratory, The US Department of Energy, Berkeley, California, USA
| | - Benjamin M Woolston
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts, USA
| |
Collapse
|
14
|
Nuhamunada M, Mohite OS, Phaneuf P, Palsson B, Weber T. BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets. Nucleic Acids Res 2024; 52:5478-5495. [PMID: 38686794 PMCID: PMC11162802 DOI: 10.1093/nar/gkae314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 03/22/2024] [Accepted: 04/11/2024] [Indexed: 05/02/2024] Open
Abstract
Genome mining is revolutionizing natural products discovery efforts. The rapid increase in available genomes demands comprehensive computational platforms to effectively extract biosynthetic knowledge encoded across bacterial pangenomes. Here, we present BGCFlow, a novel systematic workflow integrating analytics for large-scale genome mining of bacterial pangenomes. BGCFlow incorporates several genome analytics and mining tools grouped into five common stages of analysis such as: (i) data selection, (ii) functional annotation, (iii) phylogenetic analysis, (iv) genome mining, and (v) comparative analysis. Furthermore, BGCFlow provides easy configuration of different projects, parallel distribution, scheduled job monitoring, an interactive database to visualize tables, exploratory Jupyter Notebooks, and customized reports. Here, we demonstrate the application of BGCFlow by investigating the phylogenetic distribution of various biosynthetic gene clusters detected across 42 genomes of the Saccharopolyspora genus, known to produce industrially important secondary/specialized metabolites. The BGCFlow-guided analysis predicted more accurate dereplication of BGCs and guided the targeted comparative analysis of selected RiPPs. The scalable, interoperable, adaptable, re-entrant, and reproducible nature of the BGCFlow will provide an effective novel way to extract the biosynthetic knowledge from the ever-growing genomic datasets of biotechnologically relevant bacterial species.
Collapse
Affiliation(s)
- Matin Nuhamunada
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Omkar S Mohite
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Patrick V Phaneuf
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Bernhard O Palsson
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| |
Collapse
|
15
|
Hohmann M, Brunner V, Johannes W, Schum D, Carroll LM, Liu T, Sasaki D, Bosch J, Clavel T, Sieber SA, Zeller G, Tschurtschenthaler M, Janßen KP, Gulder TAM. Bacillamide D produced by Bacillus cereus from the mouse intestinal bacterial collection (miBC) is a potent cytotoxin in vitro. Commun Biol 2024; 7:655. [PMID: 38806706 PMCID: PMC11133360 DOI: 10.1038/s42003-024-06208-3] [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: 12/10/2023] [Accepted: 04/17/2024] [Indexed: 05/30/2024] Open
Abstract
The gut microbiota influences human health and the development of chronic diseases. However, our understanding of potentially protective or harmful microbe-host interactions at the molecular level is still in its infancy. To gain further insights into the hidden gut metabolome and its impact, we identified a cryptic non-ribosomal peptide BGC in the genome of Bacillus cereus DSM 28590 from the mouse intestine ( www.dsmz.de/miBC ), which was predicted to encode a thiazol(in)e substructure. Cloning and heterologous expression of this BGC revealed that it produces bacillamide D. In-depth functional evaluation showed potent cytotoxicity and inhibition of cell migration using the human cell lines HCT116 and HEK293, which was validated using primary mouse organoids. This work establishes the bacillamides as selective cytotoxins from a bacterial gut isolate that affect mammalian cells. Our targeted structure-function-predictive approach is demonstrated to be a streamlined method to discover deleterious gut microbial metabolites with potential effects on human health.
Collapse
Affiliation(s)
- Maximilian Hohmann
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069, Dresden, Germany
| | - Valentina Brunner
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, 81675, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, 81675, Munich, Germany
- Division of Translational Cancer Research German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Widya Johannes
- Department of Surgery, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, 81675, Munich, Germany
| | - Dominik Schum
- Department of Bioscience, Center for Functional Protein Assemblies, Technical University of Munich, 85748, Garching bei München, Germany
| | - Laura M Carroll
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 61997, Heidelberg, Germany
| | - Tianzhe Liu
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069, Dresden, Germany
| | - Daisuke Sasaki
- Department of Surgery, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, 81675, Munich, Germany
- Research and Development Headquarters, Nitto Boseki Co., Ltd., 102-8489, Tokyo, Japan
| | - Johanna Bosch
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, 52074, Aachen, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, 52074, Aachen, Germany
| | - Stephan A Sieber
- Department of Bioscience, Center for Functional Protein Assemblies, Technical University of Munich, 85748, Garching bei München, Germany
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 61997, Heidelberg, Germany
| | - Markus Tschurtschenthaler
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, 81675, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, 81675, Munich, Germany.
- Division of Translational Cancer Research German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120, Heidelberg, Germany.
| | - Klaus-Peter Janßen
- Department of Surgery, Klinikum rechts der Isar, School of Medicine and Health, Technical University of Munich, 81675, Munich, Germany.
| | - Tobias A M Gulder
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069, Dresden, Germany.
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Natural Product Biotechnology, Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8.1, 66123, Saarbrücken, Germany.
| |
Collapse
|
16
|
Kwon KM, Kim EH, Sim KH, Lee YJ, Kang EJ, Han KH, Jin JS, Kim DK, Ahn JH, Hwang IH. Phenylacetic acid, an anti-vaginitis metabolite produced by the vaginal symbiotic bacterium Chryseobacterium gleum. Sci Rep 2024; 14:12226. [PMID: 38806600 PMCID: PMC11133378 DOI: 10.1038/s41598-024-62947-7] [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: 07/25/2023] [Accepted: 05/22/2024] [Indexed: 05/30/2024] Open
Abstract
The human microbiome contains genetic information that regulates metabolic processes in response to host health and disease. While acidic vaginal pH is maintained in normal conditions, the pH level increases in infectious vaginitis. We propose that this change in the vaginal environment triggers the biosynthesis of anti-vaginitis metabolites. Gene expression levels of Chryseobacterium gleum, a vaginal symbiotic bacterium, were found to be affected by pH changes. The distinctive difference in the metabolic profiles between two C. gleum cultures incubated under acidic and neutral pH conditions was suggested to be an anti-vaginitis molecule, which was identified as phenylacetic acid (PAA) by spectroscopic data analysis. The antimicrobial activity of PAA was evaluated in vitro, showing greater toxicity toward Gardnerella vaginalis and Candida albicans, two major vaginal pathogens, relative to commensal Lactobacillus spp. The activation of myeloperoxidase, prostaglandin E2, and nuclear factor-κB, and the expression of cyclooxygenase-2 were reduced by an intravaginal administration of PAA in the vaginitis mouse model. In addition, PAA displayed the downregulation of mast cell activation. Therefore, PAA was suggested to be a messenger molecule that mediates interactions between the human microbiome and vaginal health.
Collapse
Affiliation(s)
- Kang Mu Kwon
- Department of Pharmacy, Woosuk University, Wanju, Jeonbuk, 55338, Republic of Korea
| | - Eun-Hye Kim
- Department of Korean Pharmacy, Woosuk University, Wanju, Jeonbuk, 55338, Republic of Korea
| | - Kyeong Hwa Sim
- Department of Pharmacology, School of Medicine, Daegu Catholic University, 33 Duryugongwon-ro 17-gil, Nam-gu, Daegu, 42472, Republic of Korea
| | - Youn Ju Lee
- Department of Pharmacology, School of Medicine, Daegu Catholic University, 33 Duryugongwon-ro 17-gil, Nam-gu, Daegu, 42472, Republic of Korea
| | - Eun-Ji Kang
- Department of Food and Biotechnology, Woosuk University, Wanju, Jeonbuk, 55338, Republic of Korea
| | - Kap-Hoon Han
- Department of Pharmaceutical Engineering, Woosuk University, Wanju, Jeonbuk, 55338, Republic of Korea
| | - Jong-Sik Jin
- Department of Oriental Medicine Resources, Jeonbuk National University, Iksan, Jeonbuk, 54596, Republic of Korea
| | - Dae Keun Kim
- Department of Pharmacy, Woosuk University, Wanju, Jeonbuk, 55338, Republic of Korea
- Research Institute of Pharmaceutical Sciences, Woosuk University, Wanju, 55338, Republic of Korea
| | - Ji-Hye Ahn
- Department of Korean Pharmacy, Woosuk University, Wanju, Jeonbuk, 55338, Republic of Korea.
| | - In Hyun Hwang
- Department of Pharmacy, Woosuk University, Wanju, Jeonbuk, 55338, Republic of Korea.
- Research Institute of Pharmaceutical Sciences, Woosuk University, Wanju, 55338, Republic of Korea.
| |
Collapse
|
17
|
Pusadkar V, Mazumder A, Azad A, Patil D, Azad RK. Deciphering Microbial Shifts in the Gut and Lung Microbiomes of COVID-19 Patients. Microorganisms 2024; 12:1058. [PMID: 38930440 PMCID: PMC11205787 DOI: 10.3390/microorganisms12061058] [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: 05/09/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
COVID-19, caused by SARS-CoV-2, results in respiratory and cardiopulmonary infections. There is an urgent need to understand not just the pathogenic mechanisms of this disease but also its impact on the physiology of different organs and microbiomes. Multiple studies have reported the effects of COVID-19 on the gastrointestinal microbiota, such as promoting dysbiosis (imbalances in the microbiome) following the disease's progression. Deconstructing the dynamic changes in microbiome composition that are specifically correlated with COVID-19 patients remains a challenge. Motivated by this problem, we implemented a biomarker discovery pipeline to identify candidate microbes specific to COVID-19. This involved a meta-analysis of large-scale COVID-19 metagenomic data to decipher the impact of COVID-19 on the human gut and respiratory microbiomes. Metagenomic studies of the gut and respiratory microbiomes of COVID-19 patients and of microbiomes from other respiratory diseases with symptoms similar to or overlapping with COVID-19 revealed 1169 and 131 differentially abundant microbes in the human gut and respiratory microbiomes, respectively, that uniquely associate with COVID-19. Furthermore, by utilizing machine learning models (LASSO and XGBoost), we demonstrated the power of microbial features in separating COVID-19 samples from metagenomic samples representing other respiratory diseases and controls (healthy individuals), achieving an overall accuracy of over 80%. Overall, our study provides insights into the microbiome shifts occurring in COVID-19 patients, shining a new light on the compositional changes.
Collapse
Affiliation(s)
- Vaidehi Pusadkar
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA;
| | - Anirudh Mazumder
- Texas Academy of Mathematics and Science, University of North Texas, Denton, TX 76203, USA
| | - Abhijay Azad
- Texas Academy of Mathematics and Science, University of North Texas, Denton, TX 76203, USA
| | - Deepti Patil
- Texas Academy of Mathematics and Science, University of North Texas, Denton, TX 76203, USA
| | - Rajeev K. Azad
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA;
| |
Collapse
|
18
|
Wu S, Zhou H, Chen D, Lu Y, Li Y, Qiao J. Multi-omic analysis tools for microbial metabolites prediction. Brief Bioinform 2024; 25:bbae264. [PMID: 38859767 PMCID: PMC11165163 DOI: 10.1093/bib/bbae264] [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: 02/03/2024] [Revised: 05/08/2024] [Indexed: 06/12/2024] Open
Abstract
How to resolve the metabolic dark matter of microorganisms has long been a challenging problem in discovering active molecules. Diverse omics tools have been developed to guide the discovery and characterization of various microbial metabolites, which make it gradually possible to predict the overall metabolites for individual strains. The combinations of multi-omic analysis tools effectively compensates for the shortcomings of current studies that focus only on single omics or a broad class of metabolites. In this review, we systematically update, categorize and sort out different analysis tools for microbial metabolites prediction in the last five years to appeal for the multi-omic combination on the understanding of the metabolic nature of microbes. First, we provide the general survey on different updated prediction databases, webservers, or software that based on genomics, transcriptomics, proteomics, and metabolomics, respectively. Then, we discuss the essentiality on the integration of multi-omics data to predict metabolites of different microbial strains and communities, as well as stressing the combination of other techniques, such as systems biology methods and data-driven algorithms. Finally, we identify key challenges and trends in developing multi-omic analysis tools for more comprehensive prediction on diverse microbial metabolites that contribute to human health and disease treatment.
Collapse
Affiliation(s)
- Shengbo Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University, Shaoxing, Shaoxing 312300, China
| | - Haonan Zhou
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Danlei Chen
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University, Shaoxing, Shaoxing 312300, China
| | - Yutong Lu
- Zhejiang Institute of Tianjin University, Shaoxing, Shaoxing 312300, China
| | - Yanni Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin 300072, China
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University, Shaoxing, Shaoxing 312300, China
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| |
Collapse
|
19
|
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.
Collapse
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.
| |
Collapse
|
20
|
Dong X, Zhang T, Wu W, Peng Y, Liu X, Han Y, Chen X, Gao Z, Xia J, Shao Z, Greening C. A vast repertoire of secondary metabolites potentially influences community dynamics and biogeochemical processes in cold seeps. SCIENCE ADVANCES 2024; 10:eadl2281. [PMID: 38669328 PMCID: PMC11051675 DOI: 10.1126/sciadv.adl2281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/27/2024] [Indexed: 04/28/2024]
Abstract
In deep-sea cold seeps, microbial communities thrive on the geological seepage of hydrocarbons and inorganic compounds, differing from photosynthetically driven ecosystems. However, their biosynthetic capabilities remain largely unexplored. Here, we analyzed 81 metagenomes, 33 metatranscriptomes, and 7 metabolomes derived from nine different cold seep areas to investigate their secondary metabolites. Cold seep microbiomes encode diverse and abundant biosynthetic gene clusters (BGCs). Most BGCs are affiliated with understudied bacteria and archaea, including key mediators of methane and sulfur cycling. The BGCs encode diverse antimicrobial compounds that potentially shape community dynamics and various metabolites predicted to influence biogeochemical cycling. BGCs from key players are widely distributed and highly expressed, with their abundance and expression levels varying with sediment depth. Sediment metabolomics reveals unique natural products, highlighting uncharted chemical potential and confirming BGC activity in these sediments. Overall, these results demonstrate that cold seep sediments serve as a reservoir of hidden natural products and sheds light on microbial adaptation in chemosynthetically driven ecosystems.
Collapse
Affiliation(s)
- Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
| | - Tianxueyu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, China
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310005, China
| | - Weichao Wu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Science, Shanghai Ocean University, Shanghai 201306, China
| | - Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Xinyue Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Yingchun Han
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Xiangwei Chen
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Zhizeng Gao
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Jinmei Xia
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| |
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Luo LM, Xu H, Zhang N, Ge H, Xiang Y, Yang H, He YX. Pyoluteorin regulates the biosynthesis of 2,4-DAPG through the TetR family transcription factor PhlH in Pseudomonas protegens Pf-5. Appl Environ Microbiol 2024; 90:e0174323. [PMID: 38470180 PMCID: PMC11022555 DOI: 10.1128/aem.01743-23] [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: 10/02/2023] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
Soil and rhizosphere bacteria act as a rich source of secondary metabolites, effectively fighting against a diverse array of pathogens. Certain Pseudomonas species harbor biosynthetic gene clusters for producing both pyoluteorin and 2,4-diacetylphloroglucinol (2,4-DAPG), which are polyketides that exhibit highly similar antimicrobial spectrum against bacteria and fungi or oomycete. A complex cross talk exists between pyoluteorin and 2,4-DAPG biosynthesis, and production of 2,4-DAPG was strongly repressed by pyoluteorin, yet the underlying mechanism is still elusive. In this study, we find that the TetR family transcription factor PhlH is involved in the cross talk between pyoluteorin and 2,4-DAPG biosynthesis. PhlH binds to a palindromic sequence within the promoter of phlG (PphlG), which encodes a C-C bond hydrolase responsible for degrading 2,4-DAPG. As a signaling molecule, pyoluteorin disrupts the PhlH-PphlG complex by binding to PhlH, leading to decreased levels of 2,4-DAPG. Proteomics data suggest that pyoluteorin regulates multiple physiological processes including fatty acid biosynthesis and transportation of taurine, siderophore, and amino acids. Our work not only reveals a novel mechanism of cross talk between pyoluteorin and 2,4-DAPG biosynthesis, but also highlights pyoluteorin's role as a messenger in the complex communication network of Pseudomonas.IMPORTANCEAntibiosis serves as a crucial defense mechanism for microbes against invasive bacteria and resource competition. These bacteria typically orchestrate the production of multiple antibiotics in a coordinated fashion, wherein the synthesis of one antibiotic inhibits the generation of another. This strategic coordination allows the bacterium to focus its resources on producing the most advantageous antibiotic under specific circumstances. However, the underlying mechanisms of distinct antibiotic production in bacterial cells remain largely elusive. In this study, we reveal that the TetR family transcription factor PhlH detects the secondary metabolite pyoluteorin and mediates the cross talk between pyoluteorin and 2,4-DAPG biosynthesis in the biocontrol strain Pseudomonas protegens Pf-5. These findings hold promise for future research, potentially informing the manipulation of these systems to enhance the effectiveness of biocontrol agents.
Collapse
Affiliation(s)
- Li-Ming Luo
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Hang Xu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Nannan Zhang
- School of Life Sciences, Anhui University, Hefei, China
| | - Honghua Ge
- School of Life Sciences, Anhui University, Hefei, China
| | - Yun Xiang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Hao Yang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- State Key Laboratory of Applied Organic Chemistry, Frontiers Science Center for Rare Isotopes, Lanzhou Magnetic Resonance Center, Lanzhou University, Lanzhou, China
| | - Yong-Xing He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- School of Veterinary Medicine and Biosecurity, Lanzhou University, Lanzhou, China
| |
Collapse
|
23
|
Kumar K, Barbora L, Moholkar VS. Genomic insights into clostridia in bioenergy production: Comparison of metabolic capabilities and evolutionary relationships. Biotechnol Bioeng 2024; 121:1298-1313. [PMID: 38047471 DOI: 10.1002/bit.28610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 10/19/2023] [Accepted: 11/16/2023] [Indexed: 12/05/2023]
Abstract
Bacteria from diverse genera, including Acetivibrio, Bacillus, Cellulosilyticum, Clostridium, Desulfotomaculum, Lachnoclostridium, Moorella, Ruminiclostridium, and Thermoanaerobacterium, have attracted significant attention due to their versatile metabolic capabilities encompassing acetogenic, cellulolytic, and C1-metabolic properties, and acetone-butanol-ethanol fermentation. Despite their biotechnological significance, a comprehensive understanding of clostridial physiology and evolution has remained elusive. This study reports an extensive comparative genomic analysis of 48 fully sequenced bacterial genomes from these genera. Our investigation, encompassing pan-genomic analysis, central carbon metabolism comparison, exploration of general genome features, and in-depth scrutiny of Cluster of Orthologous Groups genes, has established a holistic whole-genome-based phylogenetic framework. We have classified these strains into acetogenic, butanol-producing, cellulolytic, CO2-fixating, chemo(litho/organo)trophic, and heterotrophic categories, often exhibiting overlaps. Key outcomes include the identification of misclassified species and the revelation of insights into metabolic features, energy conservation, substrate utilization, stress responses, and regulatory mechanisms. These findings can provide guidance for the development of efficient microbial systems for sustainable bioenergy production. Furthermore, by addressing fundamental questions regarding genetic relationships, conserved genomic features, pivotal enzymes, and essential genes, this study has also contributed to our comprehension of clostridial biology, evolution, and their shared metabolic potential.
Collapse
Affiliation(s)
- Karan Kumar
- School of Energy Science and Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Lepakshi Barbora
- School of Energy Science and Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Vijayanand S Moholkar
- School of Energy Science and Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| |
Collapse
|
24
|
Oluwole A, Hernández-Rocamora VM, Cao Y, Li X, Vollmer W, Robinson CV, Bolla JR. Real-Time Biosynthetic Reaction Monitoring Informs the Mechanism of Action of Antibiotics. J Am Chem Soc 2024; 146:7007-7017. [PMID: 38428018 PMCID: PMC10941186 DOI: 10.1021/jacs.4c00081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 03/03/2024]
Abstract
The rapid spread of drug-resistant pathogens and the declining discovery of new antibiotics have created a global health crisis and heightened interest in the search for novel antibiotics. Beyond their discovery, elucidating mechanisms of action has necessitated new approaches, especially for antibiotics that interact with lipidic substrates and membrane proteins. Here, we develop a methodology for real-time reaction monitoring of the activities of two bacterial membrane phosphatases, UppP and PgpB. We then show how we can inhibit their activities using existing and newly discovered antibiotics such as bacitracin and teixobactin. Additionally, we found that the UppP dimer is stabilized by phosphatidylethanolamine, which, unexpectedly, enhanced the speed of substrate processing. Overall, our results demonstrate the potential of native mass spectrometry for real-time biosynthetic reaction monitoring of membrane enzymes, as well as their in situ inhibition and cofactor binding, to inform the mode of action of emerging antibiotics.
Collapse
Affiliation(s)
- Abraham
O. Oluwole
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Víctor M. Hernández-Rocamora
- Centre
for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, U.K.
| | - Yihui Cao
- Department
of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Xuechen Li
- Department
of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Waldemar Vollmer
- Centre
for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, U.K.
- Institute
for Molecular Bioscience, University of
Queensland, Carmody Road, Brisbane, Queensland 4072, Australia
| | - Carol V. Robinson
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Jani R. Bolla
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
- Department
of Biology, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K.
| |
Collapse
|
25
|
Balcha ES, Macey MC, Gemeda MT, Cavalazzi B, Woldesemayat AA. Mining the microbiome of Lake Afdera to gain insights into microbial diversity and biosynthetic potential. FEMS MICROBES 2024; 5:xtae008. [PMID: 38560625 PMCID: PMC10979467 DOI: 10.1093/femsmc/xtae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 01/24/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Microorganisms inhabiting hypersaline environments have received significant attention due to their ability to thrive under poly-extreme conditions, including high salinity, elevated temperatures and heavy metal stress. They are believed to possess biosynthetic gene clusters (BGCs) that encode secondary metabolites as survival strategy and offer potential biotechnological applications. In this study, we mined BGCs in shotgun metagenomic sequences generated from Lake Afdera, a hypersaline lake in the Afar Depression, Ethiopia. The microbiome of Lake Afdera is predominantly bacterial, with Acinetobacter (18.6%) and Pseudomonas (11.8%) being ubiquitously detected. A total of 94 distinct BGCs were identified in the metagenomic data. These BGCs are found to encode secondary metabolites with two main categories of functions: (i) potential pharmaceutical applications (nonribosomal peptide synthase NRPs, polyketide synthase, others) and (ii) miscellaneous roles conferring adaptation to extreme environment (bacteriocins, ectoine, others). Notably, NRPs (20.6%) and bacteriocins (10.6%) were the most abundant. Furthermore, our metagenomic analysis predicted gene clusters that enable microbes to defend against a wide range of toxic metals, oxidative stress and osmotic stress. These findings suggest that Lake Afdera is a rich biological reservoir, with the predicted BGCs playing critical role in the survival and adaptation of extremophiles.
Collapse
Affiliation(s)
- Ermias Sissay Balcha
- School of Medical Laboratory Science, College of Health Sciences, Hawassa University, 16417, Hawassa, Ethiopia
- Biotechnology and Bioprocess Center of Excellence, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, 16417, Addis Ababa, Ethiopia
| | - Michael C Macey
- Astrobiology OU, School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, MK7 6AA, United Kingdom
| | - Mesfin Tafesse Gemeda
- Biotechnology and Bioprocess Center of Excellence, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, 16417, Addis Ababa, Ethiopia
| | - Barbara Cavalazzi
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
- Department of Geology, University of Johannesburg, Johannesburg, South Africa
| | - Adugna Abdi Woldesemayat
- Biotechnology and Bioprocess Center of Excellence, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, 16417, Addis Ababa, Ethiopia
| |
Collapse
|
26
|
Kubiak X, Polsinelli I, Chavas LMG, Fyfe CD, Guillot A, Fradale L, Brewee C, Grimaldi S, Gerbaud G, Thureau A, Legrand P, Berteau O, Benjdia A. Structural and mechanistic basis for RiPP epimerization by a radical SAM enzyme. Nat Chem Biol 2024; 20:382-391. [PMID: 38158457 DOI: 10.1038/s41589-023-01493-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/30/2023] [Indexed: 01/03/2024]
Abstract
D-Amino acid residues, found in countless peptides and natural products including ribosomally synthesized and post-translationally modified peptides (RiPPs), are critical for the bioactivity of several antibiotics and toxins. Recently, radical S-adenosyl-L-methionine (SAM) enzymes have emerged as the only biocatalysts capable of installing direct and irreversible epimerization in RiPPs. However, the mechanism underpinning this biochemical process is ill-understood and the structural basis for this post-translational modification remains unknown. Here we report an atomic-resolution crystal structure of a RiPP-modifying radical SAM enzyme in complex with its substrate properly positioned in the active site. Crystallographic snapshots, size-exclusion chromatography-small-angle x-ray scattering, electron paramagnetic resonance spectroscopy and biochemical analyses reveal how epimerizations are installed in RiPPs and support an unprecedented enzyme mechanism for peptide epimerization. Collectively, our study brings unique perspectives on how radical SAM enzymes interact with RiPPs and catalyze post-translational modifications in natural products.
Collapse
Affiliation(s)
- Xavier Kubiak
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Ivan Polsinelli
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | | | - Cameron D Fyfe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Alain Guillot
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Laura Fradale
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Clémence Brewee
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | | | | | - Aurélien Thureau
- Synchrotron SOLEIL, HelioBio Group, L'Orme des Merisiers, Saint-Aubin, France
| | - Pierre Legrand
- Synchrotron SOLEIL, HelioBio Group, L'Orme des Merisiers, Saint-Aubin, France
| | - Olivier Berteau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France.
| | - Alhosna Benjdia
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France.
| |
Collapse
|
27
|
Hussain A, Patwekar U, Mongad DS, Nimonkar Y, Mundhe S, Paul D, Prakash O, Shouche YS. Functional antagonism and insights into the biosynthetic potential of human gut-derived microbes. Int J Antimicrob Agents 2024; 63:107091. [PMID: 38242249 DOI: 10.1016/j.ijantimicag.2024.107091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 12/09/2023] [Accepted: 01/11/2024] [Indexed: 01/21/2024]
Abstract
The specialised small molecules encoded by commensal microbes mediate distinct functional interactions. However, there is a landscape of antagonistic interactions mediated by specialised strains and their small molecules. Herein, the antagonistic landscape within a collection of 330 human gut-derived commensal microbial strains was elucidated to evaluate antimicrobial interactions as a defensive contributor, and gain new insights into structure-related functions. The potential antagonistic gut-derived strains displayed strain-specific selective inhibition. This is in contrast to common antimicrobial drugs, which typically wipe out a broad range of species and are usually found in environmental microbes. Genome sequencing of representative gut strains revealed the presence of significant biosynthetic gene clusters (BGCs) encoding compound families that contribute to antagonistic activities, and are important in host defence and maintaining gut homeostasis. Subsets of these BGCs were abundant in metagenomic sequencing data from healthy individuals. Furthermore, the cell culture secretome of these strains revealed potential biomarkers linked to hallmark pathways. These microorganisms have biosynthetic novelty and are a source of biologically significant natural products. Such natural products are essential in the development of new antimicrobial agents to reduce the usage of broad-spectrum antibiotics and combat antimicrobial resistance.
Collapse
Affiliation(s)
| | - Umera Patwekar
- NCMR- National Centre for Cell Science (NCCS), Pune- 411007, India
| | | | - Yogesh Nimonkar
- NCMR- National Centre for Cell Science (NCCS), Pune- 411007, India
| | - Swapnil Mundhe
- NCMR- National Centre for Cell Science (NCCS), Pune- 411007, India
| | - Dhiraj Paul
- NCMR- National Centre for Cell Science (NCCS), Pune- 411007, India
| | - Om Prakash
- NCMR- National Centre for Cell Science (NCCS), Pune- 411007, India
| | - Yogesh S Shouche
- NCMR- National Centre for Cell Science (NCCS), Pune- 411007, India
| |
Collapse
|
28
|
Elmassry MM, Sugihara K, Chankhamjon P, Camacho FR, Wang S, Sugimoto Y, Chatterjee S, Chen LA, Kamada N, Donia MS. A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.07.579278. [PMID: 38370680 PMCID: PMC10871352 DOI: 10.1101/2024.02.07.579278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Changes in the gut microbiome have been associated with several human diseases, but the molecular and functional details underlying these associations remain largely unknown. Here, we performed a multi-cohort analysis of small molecule biosynthetic gene clusters (BGCs) in 5,306 metagenomic samples of the gut microbiome from 2,033 Inflammatory Bowel Disease (IBD) patients and 833 matched healthy subjects and identified a group of Clostridia-derived BGCs that are significantly associated with IBD. Using synthetic biology, we discovered and solved the structures of six fatty acid amides as the products of the IBD-enriched BGCs. Using two mouse models of colitis, we show that the discovered small molecules disrupt gut permeability and exacerbate inflammation in chemically and genetically susceptible mice. These findings suggest that microbiome-derived small molecules may play a role in the etiology of IBD and represent a generalizable approach for discovering molecular mediators of microbiome-host interactions in the context of microbiome-associated diseases.
Collapse
Affiliation(s)
- Moamen M Elmassry
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA
| | - Kohei Sugihara
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | | | - Francine R Camacho
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, 08544, USA
| | - Shuo Wang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, 08544, USA
| | - Yuki Sugimoto
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA
| | - Seema Chatterjee
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA
| | - Lea Ann Chen
- Department of Medicine, Division of Gastroenterology and Hepatology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, 08901, USA
| | - Nobuhiko Kamada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Mohamed S Donia
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, 08544, USA
- Lead Contact
| |
Collapse
|
29
|
van Bergeijk DA, Augustijn HE, Elsayed SS, Willemse J, Carrión VJ, Du C, Urem M, Grigoreva LV, Cheprasov MY, Grigoriev S, Jansen H, Wintermans B, Budding AE, Spaink HP, Medema MH, van Wezel GP. Taxonomic and metabolic diversity of Actinomycetota isolated from faeces of a 28,000-year-old mammoth. Environ Microbiol 2024; 26:e16589. [PMID: 38356049 DOI: 10.1111/1462-2920.16589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/25/2024] [Indexed: 02/16/2024]
Abstract
Ancient environmental samples, including permafrost soils and frozen animal remains, represent an archive with microbial communities that have barely been explored. This yet unexplored microbial world is a genetic resource that may provide us with new evolutionary insights into recent genomic changes, as well as novel metabolic pathways and chemistry. Here, we describe Actinomycetota Micromonospora, Oerskovia, Saccharopolyspora, Sanguibacter and Streptomyces species were successfully revived and their genome sequences resolved. Surprisingly, the genomes of these bacteria from an ancient source show a large phylogenetic distance to known strains and harbour many novel biosynthetic gene clusters that may well represent uncharacterised biosynthetic potential. Metabolic profiles of the strains display the production of known molecules like antimycin, conglobatin and macrotetrolides, but the majority of the mass features could not be dereplicated. Our work provides insights into Actinomycetota isolated from an ancient source, yielding unexplored genomic information that is not yet present in current databases.
Collapse
Affiliation(s)
- Doris A van Bergeijk
- Department of Microbiology, Immunology and Transplantation (Laboratory of Molecular Bacteriology), KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Hannah E Augustijn
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | | | - Joost Willemse
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Victor J Carrión
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Department of Microbiology, University of Málaga, Málaga, Spain
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Chao Du
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Mia Urem
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | | | | | | | - Bas Wintermans
- Department of Medical Microbiology, Adrz Hospital, Goes, The Netherlands
| | | | - Herman P Spaink
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Marnix H Medema
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Gilles P van Wezel
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| |
Collapse
|
30
|
Lin XB, Liu T, Schmaltz R, Ramer-Tait AE, Walter JW, Gänzle MG. Competitiveness of reutericyclin producing and nonproducing Limosilactobacillus reuteri in food and intestinal ecosystems: a game of rock, paper, and scissors? Lett Appl Microbiol 2024; 77:ovae007. [PMID: 38244231 DOI: 10.1093/lambio/ovae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 01/22/2024]
Abstract
The ecological relationships among antimicrobial producing, resistant, and sensitive strains have been proposed to follow rock-paper-scissors dynamics, but evidence is mainly based on Gram-negative bacteriocins in vitro. The ecological relevance of antimicrobials in vivo or in situ has not been systematically studied. This study therefore aimed to analyze binary and ternary competitions among reutericyclin-producing strain Limosilactobacillus reuteri TMW1.656, its reutericyclin-resistant, nonproducing isogenic derivative L. reuteri TMW1.656∆rtcN, and the reutericyclin-sensitive, nonproducing L. reuteri TMW1.656∆rtcN∆rtcT in vitro (liquid culture and static plate), in situ (sourdough fermentation), and in vivo (gut of germ-free mice). In liquid culture, L. reuteri TMW1.656 had a higher fitness than TMW1.656∆rtcN and TMW1.656∆rtcN∆rtcT. Limosilactobacillus reuteri TMW1.656∆rtcN∆rtcT had a higher fitness than TMW1.656∆rtcN. On agar plates, L. reuteri TMW1.656 had a higher fitness than TMW1.656∆rtcN∆rtcT. In situ, reutericyclin production and resistance had no influence on the fitness of the strains. In vivo, TMW1.656 had an advantage over TMW1.656∆rtcN and TMW1.656∆rtcN∆rtcT. Ternary competitions showed reutericyclin production was ecologically beneficial in all ecosystems. The findings support the ecological importance of reutericyclin in a variety of environments/niches, providing an explanation for the acquisition of the reutericyclin gene cluster in L. reuteri and its contribution to the ecological fitness of Streptococcus mutans.
Collapse
Affiliation(s)
- Xiaoxi B Lin
- University of Alberta, Dept. of Agricultural, Food and Nutritional Scienence, Edmonton, AB T6G 2P5, Canada
| | - Tingting Liu
- University of Alberta, Dept. of Agricultural, Food and Nutritional Scienence, Edmonton, AB T6G 2P5, Canada
| | - Robert Schmaltz
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588-6205, United States
| | - Amanda E Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588-6205, United States
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE 68508, United States
| | - Jens W Walter
- University of Alberta, Dept. of Agricultural, Food and Nutritional Scienence, Edmonton, AB T6G 2P5, Canada
| | - Michael G Gänzle
- University of Alberta, Dept. of Agricultural, Food and Nutritional Scienence, Edmonton, AB T6G 2P5, Canada
- Dept. of Bioengineering and Food Science, Hubei University of Technology, Wuhan 430068, P.R. China
| |
Collapse
|
31
|
Abraham E, Lawther HA, Wang Y, Zarins-Tutt JS, Rivera GS, Wu C, Connolly JA, Florence G, Agbo M, Gao H, Goss RJM. The Identification and Heterologous Expression of the Biosynthetic Gene Cluster Encoding the Antibiotic and Anticancer Agent Marinomycin. Biomolecules 2024; 14:117. [PMID: 38254717 PMCID: PMC10813093 DOI: 10.3390/biom14010117] [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: 12/19/2023] [Revised: 12/31/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
With the rise in antimicrobial resistance, there is an urgent need for new classes of antibiotic with which to treat infectious disease. Marinomycin, a polyene antibiotic from a marine microbe, has been shown capable of killing methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium (VREF), as well as having promising activity against melanoma. An attractive solution to the photoprotection of this antibiotic has been demonstrated. Here, we report the identification and analysis of the marinomycin biosynthetic gene cluster (BGC), and the biosynthetic assembly of the macrolide. The marinomycin BGC presents a challenge in heterologous expression due to its large size and high GC content, rendering the cluster prone to rearrangement. We demonstrate the transformation of Streptomyces lividans using a construct containing the cluster, and the heterologous expression of the encoded biosynthetic machinery and production of marinomycin B.
Collapse
Affiliation(s)
- Emily Abraham
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | - Hannah A. Lawther
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | - Yunpeng Wang
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | - Joseph S. Zarins-Tutt
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | | | - Chengcang Wu
- Intact Genomics, St. Louis, MO 63132, USA (C.W.)
| | - Jack A. Connolly
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | - Gordon Florence
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | - Matthias Agbo
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | - Hong Gao
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| | - Rebecca J. M. Goss
- Department of Chemistry & BSRC, University of St. Andrews, St. Andrews KY16 9ST, UK; (E.A.); (J.A.C.)
| |
Collapse
|
32
|
Joyce SA, Clarke DJ. Microbial metabolites as modulators of host physiology. Adv Microb Physiol 2024; 84:83-133. [PMID: 38821635 DOI: 10.1016/bs.ampbs.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
The gut microbiota is increasingly recognised as a key player in influencing human health and changes in the gut microbiota have been strongly linked with many non-communicable conditions in humans such as type 2 diabetes, obesity and cardiovascular disease. However, characterising the molecular mechanisms that underpin these associations remains an important challenge for researchers. The gut microbiota is a complex microbial community that acts as a metabolic interface to transform ingested food (and other xenobiotics) into metabolites that are detected in the host faeces, urine and blood. Many of these metabolites are only produced by microbes and there is accumulating evidence to suggest that these microbe-specific metabolites do act as effectors to influence human physiology. For example, the gut microbiota can digest dietary complex polysaccharides (such as fibre) into short-chain fatty acids (SCFA) such as acetate, propionate and butyrate that have a pervasive role in host physiology from nutrition to immune function. In this review we will outline our current understanding of the role of some key microbial metabolites, such as SCFA, indole and bile acids, in human health. Whilst many studies linking microbial metabolites with human health are correlative we will try to highlight examples where genetic evidence is available to support a specific role for a microbial metabolite in host health and well-being.
Collapse
Affiliation(s)
- Susan A Joyce
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - David J Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland.
| |
Collapse
|
33
|
Hirsch P, Tagirdzhanov A, Kushnareva A, Olkhovskii I, Graf S, Schmartz GP, Hegemann JD, Bozhüyük KAJ, Müller R, Keller A, Gurevich A. ABC-HuMi: the Atlas of Biosynthetic Gene Clusters in the Human Microbiome. Nucleic Acids Res 2024; 52:D579-D585. [PMID: 37994699 PMCID: PMC10767846 DOI: 10.1093/nar/gkad1086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/18/2023] [Accepted: 10/30/2023] [Indexed: 11/24/2023] Open
Abstract
The human microbiome has emerged as a rich source of diverse and bioactive natural products, harboring immense potential for therapeutic applications. To facilitate systematic exploration and analysis of its biosynthetic landscape, we present ABC-HuMi: the Atlas of Biosynthetic Gene Clusters (BGCs) in the Human Microbiome. ABC-HuMi integrates data from major human microbiome sequence databases and provides an expansive repository of BGCs compared to the limited coverage offered by existing resources. Employing state-of-the-art BGC prediction and analysis tools, our database ensures accurate annotation and enhanced prediction capabilities. ABC-HuMi empowers researchers with advanced browsing, filtering, and search functionality, enabling efficient exploration of the resource. At present, ABC-HuMi boasts a catalog of 19 218 representative BGCs derived from the human gut, oral, skin, respiratory and urogenital systems. By capturing the intricate biosynthetic potential across diverse human body sites, our database fosters profound insights into the molecular repertoire encoded within the human microbiome and offers a comprehensive resource for the discovery and characterization of novel bioactive compounds. The database is freely accessible at https://www.ccb.uni-saarland.de/abc_humi/.
Collapse
Affiliation(s)
- Pascal Hirsch
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
| | - Azat Tagirdzhanov
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Aleksandra Kushnareva
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Ilia Olkhovskii
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Saarbrücken Graduate School of Computer Science, Saarland University, Saarbrücken 66123, Germany
| | - Simon Graf
- Department of Computer Science, Saarland University, Saarbrücken 66123, Germany
| | - Georges P Schmartz
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Department of Pharmacy, Saarland University, Saarbrücken 66123, Germany
| | - Kenan A J Bozhüyük
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Department of Pharmacy, Saarland University, Saarbrücken 66123, Germany
| | - Andreas Keller
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
| | - Alexey Gurevich
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken 66123, Germany
- Department of Computer Science, Saarland University, Saarbrücken 66123, Germany
| |
Collapse
|
34
|
Torres Salazar BO, Dema T, Schilling NA, Janek D, Bornikoel J, Berscheid A, Elsherbini AMA, Krauss S, Jaag SJ, Lämmerhofer M, Li M, Alqahtani N, Horsburgh MJ, Weber T, Beltrán-Beleña JM, Brötz-Oesterhelt H, Grond S, Krismer B, Peschel A. Commensal production of a broad-spectrum and short-lived antimicrobial peptide polyene eliminates nasal Staphylococcus aureus. Nat Microbiol 2024; 9:200-213. [PMID: 38110697 PMCID: PMC11310079 DOI: 10.1038/s41564-023-01544-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 11/03/2023] [Indexed: 12/20/2023]
Abstract
Antagonistic bacterial interactions often rely on antimicrobial bacteriocins, which attack only a narrow range of target bacteria. However, antimicrobials with broader activity may be advantageous. Here we identify an antimicrobial called epifadin, which is produced by nasal Staphylococcus epidermidis IVK83. It has an unprecedented architecture consisting of a non-ribosomally synthesized peptide, a polyketide component and a terminal modified amino acid moiety. Epifadin combines a wide antimicrobial target spectrum with a short life span of only a few hours. It is highly unstable under in vivo-like conditions, potentially as a means to limit collateral damage of bacterial mutualists. However, Staphylococcus aureus is eliminated by epifadin-producing S. epidermidis during co-cultivation in vitro and in vivo, indicating that epifadin-producing commensals could help prevent nasal S. aureus carriage. These insights into a microbiome-derived, previously unknown antimicrobial compound class suggest that limiting the half-life of an antimicrobial may help to balance its beneficial and detrimental activities.
Collapse
Affiliation(s)
- Benjamin O Torres Salazar
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Taulant Dema
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Nadine A Schilling
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Daniela Janek
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Jan Bornikoel
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Anne Berscheid
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Ahmed M A Elsherbini
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Sophia Krauss
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Simon J Jaag
- Institute of Pharmaceutical Sciences, University of Tübingen, Tübingen, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, University of Tübingen, Tübingen, Germany
| | - Min Li
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Norah Alqahtani
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Malcolm J Horsburgh
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - José Manuel Beltrán-Beleña
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Stephanie Grond
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany.
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany.
| | - Bernhard Krismer
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany.
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany.
| | - Andreas Peschel
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| |
Collapse
|
35
|
Gu Q, Yan J, Lou Y, Zhang Z, Li Y, Zhu Z, Liu M, Wu D, Liang Y, Pu J, Zhao X, Xiao H, Li P. Bacteriocins: Curial guardians of gastrointestinal tract. Compr Rev Food Sci Food Saf 2024; 23:e13292. [PMID: 38284593 DOI: 10.1111/1541-4337.13292] [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: 08/30/2023] [Revised: 12/05/2023] [Accepted: 12/14/2023] [Indexed: 01/30/2024]
Abstract
The human gastrointestinal (GI) tract microbiome secretes various metabolites that play pivotal roles in maintaining host physiological balance and influencing disease progression. Among these metabolites, bacteriocins-small, heat-stable peptides synthesized by ribosomes-are notably prevalent in the GI region. Their multifaceted benefits have garnered significant interest in the scientific community. This review comprehensively explores the methods for mining bacteriocins (traditional separation and purification, bioinformatics, and artificial intelligence), their effects on the stomach and intestines, and their complex bioactive mechanisms. These mechanisms include flora regulation, biological barrier restoration, and intervention in epithelial cell pathways. By detailing each well-documented bacteriocin, we reveal the diverse ways in which bacteriocins interact with the GI environment. Moreover, the future research direction is prospected. By further studying the function and interaction of intestinal bacteriocins, we can discover new pharmacological targets and develop drugs targeting intestinal bacteriocins to regulate and improve human health. It provides innovative ideas and infinite possibilities for further exploration, development, and utilization of bacteriocins. The inevitable fact is that the continuously exploration of bacteriocins is sure to bring the promising future for demic GI health understanding and interference strategy.
Collapse
Affiliation(s)
- Qing Gu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Jiaqian Yan
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yeqing Lou
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Zihao Zhang
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yonglu Li
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Zichun Zhu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Manman Liu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Danli Wu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Ying Liang
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Jiaqian Pu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Xiaodan Zhao
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Hang Xiao
- Department of Food Science, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Ping Li
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| |
Collapse
|
36
|
Liu X, Liu D, Tan C, Feng W. Gut microbiome-based machine learning for diagnostic prediction of liver fibrosis and cirrhosis: a systematic review and meta-analysis. BMC Med Inform Decis Mak 2023; 23:294. [PMID: 38115019 PMCID: PMC10731850 DOI: 10.1186/s12911-023-02402-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Invasive detection methods such as liver biopsy are currently the gold standard for diagnosing liver cirrhosis and can be used to determine the degree of liver fibrosis and cirrhosis. In contrast, non-invasive diagnostic methods, such as ultrasonography, elastography, and clinical prediction scores, can prevent patients from invasiveness-related discomfort and risks and are often chosen as alternative or supplementary diagnostic methods for liver fibrosis or cirrhosis. However, these non-invasive methods cannot specify the pathological grading and early diagnosis of the lesions. Recent studies have revealed that gut microbiome-based machine learning can be utilized as a non-invasive diagnostic technique for liver cirrhosis or fibrosis, but there is no evidence-based support. Therefore, this study conducted a systematic review and meta-analysis for the first time to investigate the accuracy of machine learning based on the gut microbiota in the prediction of liver fibrosis and cirrhosis. METHODS A comprehensive and systematic search of publications published before April 2th, 2023 in PubMed, Cochrane Library, Embase, and Web of Science was conducted for relevant studies on the application of gut microbiome-based metagenomic sequencing modeling technology to the diagnostic prediction of liver cirrhosis or fibrosis. A bivariate mixed-effects model and Stata software 15.0 were adopted for the meta-analysis. RESULTS Ten studies were included in the present study, involving 11 prediction trials and 838 participants, 403 of whom were fibrotic and cirrhotic patients. Meta-analysis showed the pooled sensitivity (SEN) = 0.81 [0.75, 0.85], specificity (SEP) = 0.85 [0.77, 0.91], positive likelihood ratio (PLR) = 5.5 [3.6, 8.7], negative likelihood ratio (NLR) = 0.23 [0.18, 0.29], diagnostic odds ratio (DOR) = 24 [14, 41], and area under curve (AUC) = 0.86 [0.83-0.89]. The results demonstrated that machine learning methods had excellent potential to analyze gut microbiome data and could effectively predict liver cirrhosis or fibrosis. Machine learning provides a powerful tool for non-invasive prediction and diagnosis of liver cirrhosis or liver fibrosis, with broad clinical application prospects. However, these results need to be interpreted with caution due to limited clinical data. CONCLUSION Gut microbiome-based machine learning can be utilized as a practical, non-invasive technique for the diagnostic prediction of liver cirrhosis or fibrosis. However, most of the included studies applied the random forest algorithm in modeling, so a diversified prediction system based on microorganisms is needed to improve the non-invasive detection of liver cirrhosis or fibrosis.
Collapse
Affiliation(s)
- Xiaopei Liu
- School of Basic Medicine, Shaanxi University of Chinese Medicine, Xixian Avenue, Xixian New District, Xianyang, 712046, Shaanxi Province, China
| | - Dan Liu
- Xi'an Hospital of Traditional Chinese Medicine, Xi'an, 710016, Shaanxi, China
| | - Cong'e Tan
- School of Basic Medicine, Shaanxi University of Chinese Medicine, Xixian Avenue, Xixian New District, Xianyang, 712046, Shaanxi Province, China.
| | - Wenzhe Feng
- Affiliated Hospital of Shaanxi University of Chinese Medicine, Xianyang, 712046, Shaanxi, China
| |
Collapse
|
37
|
Baindara P, Mandal SM. Gut-Antimicrobial Peptides: Synergistic Co-Evolution with Antibiotics to Combat Multi-Antibiotic Resistance. Antibiotics (Basel) 2023; 12:1732. [PMID: 38136766 PMCID: PMC10740742 DOI: 10.3390/antibiotics12121732] [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: 11/29/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Due to huge diversity and dynamic competition, the human gut microbiome produces a diverse array of antimicrobial peptides (AMPs) that play an important role in human health. The gut microbiome has an important role in maintaining gut homeostasis by the AMPs and by interacting with other human organs via established connections such as the gut-lung, and gut-brain axis. Additionally, gut AMPs play a synergistic role with other gut microbiota and antimicrobials to maintain gut homeostasis by fighting against multi-antibiotic resistance (MAR) bacteria. Further, conventional antibiotics intake creates a synergistic evolutionary pressure for gut AMPs, where antibiotics and gut AMPs fight synergistically against MAR. Overall, gut AMPs are evolving under a complex and highly synergistic co-evolutionary pressure created by the various interactions between gut microbiota, gut AMPs, and antibiotics; however, the complete mechanism is not well understood. The current review explores the synergistic action of gut AMPs and antibiotics along with possibilities to fight against MAR bacteria.
Collapse
Affiliation(s)
- Piyush Baindara
- Radiation Oncology, NextGen Precision Health, School of Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Santi M. Mandal
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India;
| |
Collapse
|
38
|
King AM, Zhang Z, Glassey E, Siuti P, Clardy J, Voigt CA. Systematic mining of the human microbiome identifies antimicrobial peptides with diverse activity spectra. Nat Microbiol 2023; 8:2420-2434. [PMID: 37973865 DOI: 10.1038/s41564-023-01524-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 10/12/2023] [Indexed: 11/19/2023]
Abstract
Human-associated bacteria secrete modified peptides to control host physiology and remodel the microbiota species composition. Here we scanned 2,229 Human Microbiome Project genomes of species colonizing skin, gastrointestinal tract, urogenital tract, mouth and trachea for gene clusters encoding RiPPs (ribosomally synthesized and post-translationally modified peptides). We found 218 lanthipeptides and 25 lasso peptides, 70 of which were synthesized and expressed in E. coli and 23 could be purified and functionally characterized. They were tested for activity against bacteria associated with healthy human flora and pathogens. New antibiotics were identified against strains implicated in skin, nasal and vaginal dysbiosis as well as from oral strains selectively targeting those in the gut. Extended- and narrow-spectrum antibiotics were found against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococci. Mining natural products produced by human-associated microbes will enable the elucidation of ecological relationships and may be a rich resource for antimicrobial discovery.
Collapse
Affiliation(s)
- Andrew M King
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhengan Zhang
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emerson Glassey
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Piro Siuti
- Synthetic Biology Group, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
39
|
Lang H, Liu Y, Duan H, Zhang W, Hu X, Zheng H. Identification of peptides from honeybee gut symbionts as potential antimicrobial agents against Melissococcus plutonius. Nat Commun 2023; 14:7650. [PMID: 38001079 PMCID: PMC10673953 DOI: 10.1038/s41467-023-43352-6] [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: 08/11/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Eusocial pollinators are crucial elements in global agriculture. The honeybees and bumblebees are associated with a simple yet host-restricted gut community, which protect the hosts against pathogen infections. Recent genome mining has led to the discovery of biosynthesis pathways of bioactive natural products mediating microbe-microbe interactions from the gut microbiota. Here, we investigate the diversity of biosynthetic gene clusters in the bee gut microbiota by analyzing 477 genomes from cultivated bacteria and metagenome-assembled genomes. We identify 744 biosynthetic gene clusters (BGCs) covering multiple chemical classes. While gene clusters for the post-translationally modified peptides are widely distributed in the bee guts, the distribution of the BGC classes varies significantly in different bee species among geographic locations, which is attributed to the strain-level variation of bee gut members in the chemical repertoire. Interestingly, we find that Gilliamella strains possessing a thiopeptide-like BGC show potent activity against the pathogenic Melissococcus plutonius. The spectrometry-guided genome mining reveals a RiPP-encoding BGC from Gilliamella with a 10 amino acid-long core peptide exhibiting antibacterial potentials. This study illustrates the widespread small-molecule-encoding BGCs in the bee gut symbionts and provides insights into the bacteria-derived natural products as potential antimicrobial agents against pathogenic infections.
Collapse
Affiliation(s)
- Haoyu Lang
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Yuwen Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Huijuan Duan
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Wenhao Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Xiaosong Hu
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Hao Zheng
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China.
| |
Collapse
|
40
|
Upfold J, Rejasse A, Nielsen-Leroux C, Jensen AB, Sanchis-Borja V. The immunostimulatory role of an Enterococcus-dominated gut microbiota in host protection against bacterial and fungal pathogens in Galleria mellonella larvae. FRONTIERS IN INSECT SCIENCE 2023; 3:1260333. [PMID: 38469511 PMCID: PMC10926436 DOI: 10.3389/finsc.2023.1260333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/09/2023] [Indexed: 03/13/2024]
Abstract
Understanding the intricate interplay between the gut microbiota and the immune response in insects is crucial, given its diverse impact on the pathogenesis of various microbial species. The microbiota's modulation of the host immune system is one such mechanism, although its complete impact on immune responses remains elusive. This study investigated the tripartite interaction between the gut microbiota, pathogens, and the host's response in Galleria mellonella larvae reared under axenic (sterile) and conventional (non-sterile) conditions. The influence of the microbiota on host fitness during infections was evaluated via two different routes: oral infection induced by Bacillus thuringiensis subsp. galleriae (Btg), and topical infection induced by Metarhizium robertsii (Mr). We observed that larvae without a microbiota can successfully fulfill their life cycle, albeit with more variation in their developmental time. We subsequently performed survival assays on final-instar larvae, using the median lethal dose (LD50) of Btg and Mr. Our findings indicated that axenic larvae were more vulnerable to an oral infection of Btg; specifically, a dose that was calculated to be half-lethal for the conventional group resulted in a 90%-100% mortality rate in the axenic group. Through a dual-analysis experimental design, we could identify the status of the gut microbiota using 16S rRNA sequencing and assess the level of immune-related gene expression in the same group of larvae at basal conditions and during infection. This analysis revealed that the microbiota of our conventionally reared population was dominated entirely by four Enterococcus species, and these species potentially stimulated the immune response in the gut, due to the increased basal expression of two antimicrobial peptides (AMPs)-gallerimycin and gloverin-in the conventional larvae compared with the axenic larvae. Furthermore, Enterococcus mundtii, isolated from the gut of conventional larvae, showed inhibition activity against Btg in vitro. Lastly, other immune effectors, namely, phenoloxidase activity in the hemolymph and total reactive oxygen/nitrogen species (ROS/RNS) in the gut, were tested to further investigate the extent of the stimulation of the microbiota on the immune response. These findings highlight the immune-modulatory role of the Enterococcus-dominated gut microbiota, an increasingly reported microbiota assemblage of laboratory populations of Lepidoptera, and its influence on the host's response to oral and topical infections.
Collapse
Affiliation(s)
- Jennifer Upfold
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Agnès Rejasse
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | | | - Annette Bruun Jensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Vincent Sanchis-Borja
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| |
Collapse
|
41
|
Redick MA, Cummings ME, Neuhaus GF, Ardor Bellucci LM, Thurber AR, McPhail KL. Integration of Untargeted Metabolomics and Microbial Community Analyses to Characterize Distinct Deep-Sea Methane Seeps. FRONTIERS IN MARINE SCIENCE 2023; 10:1197338. [PMID: 39268414 PMCID: PMC11392061 DOI: 10.3389/fmars.2023.1197338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/15/2024]
Abstract
Deep-sea methane seeps host highly diverse microbial communities whose biological diversity is distinct from other marine habitats. Coupled with microbial community analysis, untargeted metabolomics of environmental samples using high resolution tandem mass spectrometry provides unprecedented access to the unique specialized metabolisms of these chemosynthetic microorganisms. In addition, the diverse microbial natural products are of broad interest due to their potential applications for human and environmental health and well-being. In this exploratory study, sediment cores were collected from two methane seeps (-1000 m water depth) with very different gross geomorphologies, as well as a non-seep control site. Cores were subjected to parallel metabolomic and microbial community analyses to assess the feasibility of representative metabolite detection and identify congruent patterns between metabolites and microbes. Metabolomes generated using high resolution liquid chromatography tandem mass spectrometry were annotated with predicted structure classifications of the majority of mass features using SIRIUS and CANOPUS. The microbiome was characterized by analysis of 16S rRNA genes and analyzed both at the whole community level, as well as the small subgroup of Actinobacteria, which are known to produce societally useful compounds. Overall, the younger Dagorlad seep possessed a greater abundance of metabolites while there was more variation in abundance, number, and distribution of metabolites between samples at the older Emyn Muil seep. Lipid and lipid-like molecules displayed the greatest variation between sites and accounted for a larger proportion of metabolites found at the older seep. Overall, significant differences in composition of the microbial community mirrored the patterns of metabolite diversity within the samples; both varied greatly as a function of distance from methane seep, indicating a deterministic role of seepage. Interdisciplinary research to understand microbial and metabolic diversity is essential for understanding the processes and role of ubiquitous methane seeps in global systems and here we increase understanding of these systems by visualizing some of the chemical diversity that seeps add to marine systems.
Collapse
Affiliation(s)
- Margaret A Redick
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - Milo E Cummings
- Department of Microbiology, College of Science, Oregon State University, Corvallis, Oregon, USA
| | - George F Neuhaus
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - Lila M Ardor Bellucci
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Andrew R Thurber
- Department of Microbiology, College of Science, Oregon State University, Corvallis, Oregon, USA
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| |
Collapse
|
42
|
Leonov GE, Varaeva YR, Livantsova EN, Starodubova AV. The Complicated Relationship of Short-Chain Fatty Acids and Oral Microbiome: A Narrative Review. Biomedicines 2023; 11:2749. [PMID: 37893122 PMCID: PMC10604844 DOI: 10.3390/biomedicines11102749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/30/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
The human oral microbiome has emerged as a focal point of research due to its profound implications for human health. The involvement of short-chain fatty acids in oral microbiome composition, oral health, and chronic inflammation is gaining increasing attention. In this narrative review, the results of early in vitro, in vivo, and pilot clinical studies and research projects are presented in order to define the boundaries of this new complicated issue. According to the results, the current research data are disputable and ambiguous. When investigating the role of SCFAs in human health and disease, it is crucial to distinguish between their local GI effects and the systemic influences. Locally, SCFAs are a part of normal oral microbiota metabolism, but the increased formation of SCFAs usually attribute to dysbiosis; excess SCFAs participate in the development of local oral diseases and in oral biota gut colonization and dysbiosis. On the other hand, a number of studies have established the positive impact of SCFAs on human health as a whole, including the reduction of chronic systemic inflammation, improvement of metabolic processes, and decrease of some types of cancer incidence. Thus, a complex and sophisticated approach with consideration of origin and localization for SCFA function assessment is demanded. Therefore, more research, especially clinical research, is needed to investigate the complicated relationship of SCFAs with health and disease and their potential role in prevention and treatment.
Collapse
Affiliation(s)
- Georgy E Leonov
- Federal Research Center of Nutrition, Biotechnology and Food Safety, 109240 Moscow, Russia
| | - Yurgita R Varaeva
- Federal Research Center of Nutrition, Biotechnology and Food Safety, 109240 Moscow, Russia
| | - Elena N Livantsova
- Federal Research Center of Nutrition, Biotechnology and Food Safety, 109240 Moscow, Russia
| | - Antonina V Starodubova
- Federal Research Center of Nutrition, Biotechnology and Food Safety, 109240 Moscow, Russia
- Therapy Faculty, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| |
Collapse
|
43
|
Rajput A, Chauhan SM, Mohite OS, Hyun JC, Ardalani O, Jahn LJ, Sommer MO, Palsson BO. Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family. Food Microbiol 2023; 115:104334. [PMID: 37567624 DOI: 10.1016/j.fm.2023.104334] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/29/2023] [Accepted: 07/05/2023] [Indexed: 08/13/2023]
Abstract
Lactobacillaceae represent a large family of important microbes that are foundational to the food industry. Many genome sequences of Lactobacillaceae strains are now available, enabling us to conduct a comprehensive pangenome analysis of this family. We collected 3591 high-quality genomes from public sources and found that: 1) they contained enough genomes for 26 species to perform a pangenomic analysis, 2) the normalized Heap's coefficient λ (a measure of pangenome openness) was found to have an average value of 0.27 (ranging from 0.07 to 0.37), 3) the pangenome openness was correlated with the abundance and genomic location of transposons and mobilomes, 4) the pangenome for each species was divided into core, accessory, and rare genomes, that highlight the species-specific properties (such as motility and restriction-modification systems), 5) the pangenome of Lactiplantibacillus plantarum (which contained the highest number of genomes found amongst the 26 species studied) contained nine distinct phylogroups, and 6) genome mining revealed a richness of detected biosynthetic gene clusters, with functions ranging from antimicrobial and probiotic to food preservation, but ∼93% were of unknown function. This study provides the first in-depth comparative pangenomics analysis of the Lactobacillaceae family.
Collapse
Affiliation(s)
- Akanksha Rajput
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Siddharth M Chauhan
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Omkar S Mohite
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Jason C Hyun
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA
| | - Omid Ardalani
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Leonie J Jahn
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Morten Oa Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark.
| |
Collapse
|
44
|
Santos-Júnior CD, Der Torossian Torres M, Duan Y, del Río ÁR, Schmidt TS, Chong H, Fullam A, Kuhn M, Zhu C, Houseman A, Somborski J, Vines A, Zhao XM, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP. Computational exploration of the global microbiome for antibiotic discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555663. [PMID: 37693522 PMCID: PMC10491242 DOI: 10.1101/2023.08.31.555663] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a machine learning-based approach to predict prokaryotic antimicrobial peptides (AMPs) by leveraging a vast dataset of 63,410 metagenomes and 87,920 microbial genomes. This led to the creation of AMPSphere, a comprehensive catalog comprising 863,498 non-redundant peptides, the majority of which were previously unknown. We observed that AMP production varies by habitat, with animal-associated samples displaying the highest proportion of AMPs compared to other habitats. Furthermore, within different human-associated microbiota, strain-level differences were evident. To validate our predictions, we synthesized and experimentally tested 50 AMPs, demonstrating their efficacy against clinically relevant drug-resistant pathogens both in vitro and in vivo. These AMPs exhibited antibacterial activity by targeting the bacterial membrane. Additionally, AMPSphere provides valuable insights into the evolutionary origins of peptides. In conclusion, our approach identified AMP sequences within prokaryotic microbiomes, opening up new avenues for the discovery of antibiotics.
Collapse
Affiliation(s)
- Célio Dias Santos-Júnior
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
| | - Marcelo Der Torossian Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, Pennsylvania, United States of America
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania; Philadelphia, Pennsylvania, United States of America
- Penn Institute for Computational Science, University of Pennsylvania; Philadelphia, Pennsylvania, United States of America
| | - Yiqian Duan
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
| | - Álvaro Rodríguez del Río
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Thomas S.B. Schmidt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Hui Chong
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
| | - Anthony Fullam
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael Kuhn
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Chengkai Zhu
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
| | - Amy Houseman
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
| | - Jelena Somborski
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
| | - Anna Vines
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- International Human Phenome Institute, Shanghai, China
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, Pennsylvania, United States of America
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania; Philadelphia, Pennsylvania, United States of America
- Penn Institute for Computational Science, University of Pennsylvania; Philadelphia, Pennsylvania, United States of America
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
| |
Collapse
|
45
|
Machado M, Silva S, Costa EM. Are Antimicrobial Peptides a 21st-Century Solution for Atopic Dermatitis? Int J Mol Sci 2023; 24:13460. [PMID: 37686269 PMCID: PMC10488019 DOI: 10.3390/ijms241713460] [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: 08/01/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Atopic dermatitis (AD) is a chronic inflammatory skin disorder that is the result of various environmental, bacterial and genetic stimuli, which culminate in the disruption of the skin's barrier function. Characterized by highly pruritic skin lesions, xerosis and an array of comorbidities among which skin infections are the most common, this condition results in both a significant loss of quality of life and in the need for life-long treatments (e.g., corticosteroids, monoclonal antibodies and regular antibiotic intake), all of which may have harmful secondary effects. This, in conjunction with AD's rising prevalence, made the development of alternative treatment strategies the focus of both the scientific community and the pharmaceutical industry. Given their potential to both manage the skin microbiome, fight infections and even modulate the local immune response, the use of antimicrobial peptides (AMPs) from more diverse origins has become one of the most promising alternative solutions for AD management, with some being already used with some success towards this end. However, their production and use also exhibit some limitations. The current work seeks to compile the available information and provide a better understanding of the state of the art in the understanding of AMPs' true potential in addressing AD.
Collapse
Affiliation(s)
| | - Sara Silva
- CBQF Centro de Biotecnologia e Química Fina Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal;
| | - Eduardo M. Costa
- CBQF Centro de Biotecnologia e Química Fina Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal;
| |
Collapse
|
46
|
Schluter J, Djukovic A, Taylor BP, Yan J, Duan C, Hussey GA, Liao C, Sharma S, Fontana E, Amoretti LA, Wright RJ, Dai A, Peled JU, Taur Y, Perales MA, Siranosian BA, Bhatt AS, van den Brink MRM, Pamer EG, Xavier JB. The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia. Cell Host Microbe 2023; 31:1126-1139.e6. [PMID: 37329880 PMCID: PMC10527165 DOI: 10.1016/j.chom.2023.05.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 09/28/2022] [Accepted: 05/24/2023] [Indexed: 06/19/2023]
Abstract
Longitudinal microbiome data provide valuable insight into disease states and clinical responses, but they are challenging to mine and view collectively. To address these limitations, we present TaxUMAP, a taxonomically informed visualization for displaying microbiome states in large clinical microbiome datasets. We used TaxUMAP to chart a microbiome atlas of 1,870 patients with cancer during therapy-induced perturbations. Bacterial density and diversity were positively associated, but the trend was reversed in liquid stool. Low-diversity states (dominations) remained stable after antibiotic treatment, and diverse communities had a broader range of antimicrobial resistance genes than dominations. When examining microbiome states associated with risk for bacteremia, TaxUMAP revealed that certain Klebsiella species were associated with lower risk for bacteremia localize in a region of the atlas that is depleted in high-risk enterobacteria. This indicated a competitive interaction that was validated experimentally. Thus, TaxUMAP can chart comprehensive longitudinal microbiome datasets, enabling insights into microbiome effects on human health.
Collapse
Affiliation(s)
- Jonas Schluter
- Institute for Systems Genetics, Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA.
| | - Ana Djukovic
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Bradford P Taylor
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jinyuan Yan
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Caichen Duan
- Institute for Systems Genetics, Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Grant A Hussey
- Institute for Systems Genetics, Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Chen Liao
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Sneh Sharma
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Emily Fontana
- Department of Immunology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Luigi A Amoretti
- Department of Immunology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Roberta J Wright
- Department of Immunology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Anqi Dai
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan U Peled
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA
| | - Ying Taur
- Department of Immunology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Miguel-Angel Perales
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA
| | | | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA; Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA; Department of Medicine, Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Marcel R M van den Brink
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA
| | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Joao B Xavier
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
47
|
Fernandez-Cantos MV, Garcia-Morena D, Yi Y, Liang L, Gómez-Vázquez E, Kuipers OP. Bioinformatic mining for RiPP biosynthetic gene clusters in Bacteroidales reveals possible new subfamily architectures and novel natural products. Front Microbiol 2023; 14:1219272. [PMID: 37469430 PMCID: PMC10352776 DOI: 10.3389/fmicb.2023.1219272] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/16/2023] [Indexed: 07/21/2023] Open
Abstract
The Bacteroidales order, widely distributed among diverse human populations, constitutes a key component of the human microbiota. Members of this Gram-negative order have been shown to modulate the host immune system, play a fundamental role in the gut's microbial food webs, or be involved in pathogenesis. Bacteria inhabiting such a complex environment as the human microbiome are expected to display social behaviors and, hence, possess factors that mediate cooperative and competitive interactions. Different types of molecules can mediate interference competition, including non-ribosomal peptides (NRPs), polyketides, and bacteriocins. The present study investigates the potential of Bacteroidales bacteria to biosynthesize class I bacteriocins, which are ribosomally synthesized and post-translationally modified peptides (RiPPs). For this purpose, 1,136 genome-sequenced strains from this order were mined using BAGEL4. A total of 1,340 areas of interest (AOIs) were detected. The most commonly identified enzymes involved in RiPP biosynthesis were radical S-adenosylmethionine (rSAM), either alone or in combination with other biosynthetic enzymes such as YcaO. A more comprehensive analysis of a subset of 9 biosynthetic gene clusters (BGCs) revealed a consistent association in Bacteroidales BGCs between peptidase-containing ATP-binding transporters (PCATs) and precursor peptides with GG-motifs. This finding suggests a possibly shared mechanism for leader peptide cleavage and transport of mature products. Notably, human metagenomic studies showed a high prevalence and abundance of the RiPP BGCs from Phocaeicola vulgatus and Porphyromonas gulae. The mature product of P. gulae BGC is hypothesized to display γ-thioether linkages and a C-terminal backbone amidine, a potential new combination of post-translational modifications (PTM). All these findings highlight the RiPP biosynthetic potential of Bacteroidales bacteria, as a rich source of novel peptide structures of possible relevance in the human microbiome context.
Collapse
Affiliation(s)
- Maria Victoria Fernandez-Cantos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Diego Garcia-Morena
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Yunhai Yi
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | | | - Emilio Gómez-Vázquez
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| |
Collapse
|
48
|
Konwar AN, Basak S, Devi SG, Borah JC, Thakur D. Streptomyces sp. MNP32, a forest-dwelling Actinomycetia endowed with potent antibacterial metabolites. 3 Biotech 2023; 13:257. [PMID: 37405270 PMCID: PMC10314884 DOI: 10.1007/s13205-023-03670-4] [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: 11/03/2022] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
The Actinomycetia isolate, MNP32 was isolated from the Manas National Park of Assam, India, located in the Indo-Burma biodiversity hotspot region of Northeast India. Morphological observations and molecular characterization revealed its identity to be Streptomyces sp. with a 99.86% similar to Streptomyces camponoticapitis strain I4-30 through 16S rRNA gene sequencing. The strain exhibited broad-spectrum antimicrobial activity against a wide range of bacterial human pathogens including WHO-listed critical priority pathogens such as methicillin-resistant Staphylococcus aureus (MRSA) and Acinetobacter baumannii. The ethyl acetate extract was found to disrupt the membrane of the test pathogens which was evidenced through scanning electron microscopy, membrane disruption assay and confocal microscopy. Cytotoxicity studies against CC1 hepatocytes demonstrated that EA-MNP32 had a negligible effect on cell viability. Chemical analysis of the bioactive fraction using gas chromatography-mass spectrometry (GC-MS) showed the presence of 2 major chemical compounds that include Phenol, 3,5-bis(1,1-dimethylethyl)- and [1,1'-Biphenyl]-2,3'-diol, 3,4',5,6'-tetrakis(1,1-dimethylethyl)- which have been reported to possess antimicrobial activity. The phenolic hydroxyl groups of these compounds were proposed to interact with the carbonyl group of the cytoplasmic proteins and lipids leading to destabilization and rupture of the cell membrane. These findings highlight the potential of exploring culturable actinobacteria from the microbiologically under-explored forest ecosystem of Northeast India and bioactive compounds from MNP32 which can be beneficial for future antibacterial drug development.
Collapse
Affiliation(s)
- Aditya Narayan Konwar
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Studies in Science and Technology, Guwahati, Assam 781035 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Surajit Basak
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Studies in Science and Technology, Guwahati, Assam 781035 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Shalini Gurumayum Devi
- Chemical Biology Laboratory-1, Life Sciences Division, Institute of Advanced Studies in Science and Technology, Guwahati, Assam 781035 India
| | - Jagat Chandra Borah
- Chemical Biology Laboratory-1, Life Sciences Division, Institute of Advanced Studies in Science and Technology, Guwahati, Assam 781035 India
| | - Debajit Thakur
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Studies in Science and Technology, Guwahati, Assam 781035 India
| |
Collapse
|
49
|
Zhang JW, Wang R, Liang X, Han P, Zheng YL, Li XF, Gao DZ, Liu M, Hou LJ, Dong HP. Novel Gene Clusters for Natural Product Synthesis Are Abundant in the Mangrove Swamp Microbiome. Appl Environ Microbiol 2023; 89:e0010223. [PMID: 37191511 PMCID: PMC10304795 DOI: 10.1128/aem.00102-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/21/2023] [Indexed: 05/17/2023] Open
Abstract
Natural microbial communities produce a diverse array of secondary metabolites with ecologically and biotechnologically relevant activities. Some of them have been used clinically as drugs, and their production pathways have been identified in a few culturable microorganisms. However, since the vast majority of microorganisms in nature have not been cultured, identifying the synthetic pathways of these metabolites and tracking their hosts remain a challenge. The microbial biosynthetic potential of mangrove swamps remains largely unknown. Here, we examined the diversity and novelty of biosynthetic gene clusters in dominant microbial populations in mangrove wetlands by mining 809 newly reconstructed draft genomes and probing the activities and products of these clusters by using metatranscriptomic and metabolomic techniques. A total of 3,740 biosynthetic gene clusters were identified from these genomes, including 1,065 polyketide and nonribosomal peptide gene clusters, 86% of which showed no similarity to known clusters in the Minimum Information about a Biosynthetic Gene Cluster (MIBiG) repository. Of these gene clusters, 59% were harbored by new species or lineages of Desulfobacterota-related phyla and Chloroflexota, whose members are highly abundant in mangrove wetlands and for which few synthetic natural products have been reported. Metatranscriptomics revealed that most of the identified gene clusters were active in field and microcosm samples. Untargeted metabolomics was also used to identify metabolites from the sediment enrichments, and 98% of the mass spectra generated were unrecognizable, further supporting the novelty of these biosynthetic gene clusters. Our study taps into a corner of the microbial metabolite reservoir in mangrove swamps, providing clues for the discovery of new compounds with valuable activities. IMPORTANCE At present, the majority of known clinical drugs originated from cultivated species of a few bacterial lineages. It is vital for the development of new pharmaceuticals to explore the biosynthetic potential of naturally uncultivable microorganisms using new techniques. Based on the large numbers of genomes reconstructed from mangrove wetlands, we identified abundant and diverse biosynthetic gene clusters in previously unsuspected phylogenetic groups. These gene clusters exhibited a variety of organizational architectures, especially for nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS), implying the presence of new compounds with valuable activities in the mangrove swamp microbiome.
Collapse
Affiliation(s)
- Jia-Wei Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Ran Wang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Ping Han
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, China
| | - Yan-Ling Zheng
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, China
| | - Xiao-Fei Li
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Deng-Zhou Gao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Min Liu
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, China
| | - Li-Jun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Hong-Po Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| |
Collapse
|
50
|
Byun H, Brockett MR, Pu Q, Hrycko AJ, Beld J, Zhu J. An Intestinal Bacillus velezensis Isolate Displays Broad-Spectrum Antibacterial Activity and Prevents Infection of Both Gram-Positive and Gram-Negative Pathogens In Vivo. J Bacteriol 2023; 205:e0013323. [PMID: 37195186 PMCID: PMC10294632 DOI: 10.1128/jb.00133-23] [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: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/18/2023] Open
Abstract
The increasing prevalence of drug-resistant bacteria has significantly diminished the effectiveness of antibiotics in clinical settings, leading to the emergence of untreatable bacterial infections. To address this public health challenge, the gut microbiome represents a promising source of novel antimicrobial therapeutics. In this study, we screened mouse intestinal isolates for growth inhibitory activity against the human enteric pathogen Vibrio cholerae and identified a strain of spore-forming Bacillus velezensis, named BVM7, that produced a potent antibiotic with activity against V. cholerae and a broad spectrum of enteric and opportunistic pathogens. Characterization of the antimicrobial compounds produced by BVM7 revealed that they were primarily secreted antimicrobial peptides (AMPs) produced during stationary-phase growth. Furthermore, our results showed that introducing either BVM7 vegetative cells or spores into mice precolonized with V. cholerae or Enterococcus faecalis significantly reduced the burden of infection. Interestingly, we also observed that BVM7 was sensitive to a group of Lactobacillus probiotic strains and that inoculation of Lactobacilli could eliminate BVM7 and potentially restore the native gut microbiome. These findings highlight the potential of bacteria from the gut microbiome as a source for novel antimicrobial compounds and a tool for managing bacterial infections by in situ bio-delivery of multiple AMPs. IMPORTANCE The rise of antibiotic-resistant pathogens poses a challenge to public health. The gut microbiome presents a promising source of new antimicrobials and treatments. By screening murine gut commensals, we found a spore-forming Bacillus velezensis strain, BVM7, that exhibited antimicrobial activity toward a wide array of enteric and opportunistic bacterial pathogens. In addition to showing that this killing effect occurred through the action of secreted antimicrobial peptides (AMPs), we demonstrate that BVM7 vegetative cells and spores can be used to treat infections of both Gram-positive and Gram-negative pathogens in vivo. By expanding our knowledge of the antimicrobial properties of bacteria in the gut microbiome, we hope to contribute insights for developing novel drugs and therapeutic interventions.
Collapse
Affiliation(s)
- Hyuntae Byun
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mary R. Brockett
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Qinqin Pu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrew J. Hrycko
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Joris Beld
- Department of Microbiology & Immunology, College of Medicine, Drexel University, Philadelphia, Pennsylvania, USA
| | - Jun Zhu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| |
Collapse
|