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Muhammad N, Avila F, Kim SG. Comparative genome analysis of the genus Marivirga and proposal of two novel marine species: Marivirga arenosa sp. nov., and Marivirga salinae sp. nov. BMC Microbiol 2024; 24:245. [PMID: 38970021 PMCID: PMC11225308 DOI: 10.1186/s12866-024-03393-3] [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: 04/14/2024] [Accepted: 06/20/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND The phylum Bacteroidota represents a significant proportion of heterotrophic bacteria found in marine ecosystems. Members of the phylum Bacteroidota are actively involved in the degradation of biopolymers such as polysaccharides and proteins. Bacteroidota genomes exhibit a significant enrichment of various enzymes, including carbohydrate-active enzymes (CAZymes), carboxypeptidases, esterases, isomerases, peptidases, phosphatases, and sulfatases. The genus Marivirga, a member of the family Marivirgaceae within the phylum Bacteroidota, comprises six documented species. During a microbial diversity study, three novel Marivirga strains (BKB1-2 T, ABR2-2, and BDSF4-3 T) were isolated from the West Sea, Republic of Korea. RESULTS To explore the taxonomic status and genomic characteristics of the novel isolates, we employed a polyphasic taxonomic approach, which included phylogenetic, chemotaxonomic and comprehensive genome analysis. The three isolates were Gram-stain-negative, aerobic, rod-shaped, moderately halophilic, and had a gliding motility. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among the two isolates, BKB1-2 T and BDSF4-3 T, and the six reference strains were 70.5-76.5% for ANI and 18.1-25.7% for dDDH. Interestingly, the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the strains harbor genes for a comprehensive pathway for dissimilatory nitrate reduction to ammonium (DNRA), as well as other nitrogen pathways for the reduction of nitrite, nitric oxide, and nitrous oxide. Additionally, the antiSMASH analysis indicated that the strains contained three to eight biosynthetic gene clusters (BGCs) associated with the synthesis of secondary metabolites. Furthermore, the strains carried a high number of CAZyme ranging from 53 to 152, which was also demonstrated by an in vitro analysis of degradation of the polysaccharide cellulose, chitin, laminarin, starch, and xylan. Additionally, all the strains carried genes for the metabolism of heavy metals, and exhibited tolerance to heavy metals, with minimum inhibitory concentrations (MICs) in millimoles (mM) in ranges of Co2+ (3-6), Cu2+ (0.2-0.4), Ni2+ (3-5), Zn2+ (2-4), Mn2+ (20-50), and Hg2+ (0.3). CONCLUSIONS Based on polyphasic taxonomic approach, the three isolated strains represent two novel species names Marivirga arenosa sp. nov. (BKB1-2 T = KCTC 82989 T = InaCC B1618T), and Marivirga salinae sp. nov. (BDSF4-3 T = KCTC 82973 T = InaCC B1619T).
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Affiliation(s)
- Neak Muhammad
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea ResearchInstitute of Bioscience and Biotechnology, Jeongeup, Jeonbuk, 56212, the Republic of Korea
- Department of Biotechnology, KRIBB School, University of Science and Technology (UST), Daejeon, 34113, the Republic of Korea
| | - Forbes Avila
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea ResearchInstitute of Bioscience and Biotechnology, Jeongeup, Jeonbuk, 56212, the Republic of Korea
- Department of Biotechnology, KRIBB School, University of Science and Technology (UST), Daejeon, 34113, the Republic of Korea
| | - Song-Gun Kim
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea ResearchInstitute of Bioscience and Biotechnology, Jeongeup, Jeonbuk, 56212, the Republic of Korea.
- Department of Biotechnology, KRIBB School, University of Science and Technology (UST), Daejeon, 34113, the Republic of Korea.
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Riyanti, Zumkeller CM, Spohn M, Mihajlovic S, Schwengers O, Goesmann A, Riviani R, Meinita MDN, Hastuti DWB, Prihatiningsih I, Dewi R, Schäberle TF. Draft genome sequence of Galbibacter sp. PAP.153, isolated from a marine sponge in Papua, Indonesia. Microbiol Resour Announc 2024; 13:e0129723. [PMID: 38988209 PMCID: PMC11237725 DOI: 10.1128/mra.01297-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 04/15/2024] [Indexed: 07/12/2024] Open
Abstract
Galbibacter sp. PAP.153 was isolated from a marine sponge. Here, we report its 4.12 Mbp draft genome sequence and rate its specialized metabolite production capacity with specific focus on the chemotaxonomic marker flexirubin.
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Affiliation(s)
- Riyanti
- Faculty of Fisheries and Marine Science, Jenderal Soedirman University, Purwokerto, Indonesia
| | - Celine M Zumkeller
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | - Marius Spohn
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | - Sanja Mihajlovic
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Oliver Schwengers
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Braunschweig, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Braunschweig, Germany
| | - Riviani Riviani
- Faculty of Fisheries and Marine Science, Jenderal Soedirman University, Purwokerto, Indonesia
| | - Maria Dyah Nur Meinita
- Faculty of Fisheries and Marine Science, Jenderal Soedirman University, Purwokerto, Indonesia
| | | | - Isnaini Prihatiningsih
- Faculty of Fisheries and Marine Science, Jenderal Soedirman University, Purwokerto, Indonesia
| | - Rose Dewi
- Faculty of Fisheries and Marine Science, Jenderal Soedirman University, Purwokerto, Indonesia
| | - Till F Schäberle
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Braunschweig, Germany
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3
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Russ L, Andreo Jimenez B, Nijhuis E, Postma J. Rhizoctonia solani disease suppression: addition of keratin-rich soil amendment leads to functional shifts in soil microbial communities. FEMS Microbiol Ecol 2024; 100:fiae024. [PMID: 38499445 PMCID: PMC10959553 DOI: 10.1093/femsec/fiae024] [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: 10/12/2023] [Revised: 02/06/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024] Open
Abstract
Promoting soil suppressiveness against soil borne pathogens could be a promising strategy to manage crop diseases. One way to increase the suppression potential in agricultural soils is via the addition of organic amendments. This microbe-mediated phenomenon, although not fully understood, prompted our study to explore the microbial taxa and functional properties associated with Rhizoctonia solani disease suppression in sugar beet seedlings after amending soil with a keratin-rich waste stream. Soil samples were analyzed using shotgun metagenomics sequencing. Results showed that both amended soils were enriched in bacterial families found in disease suppressive soils before, indicating that the amendment of keratin-rich material can support the transformation into a suppressive soil. On a functional level, genes encoding keratinolytic enzymes were found to be abundant in the keratin-amended samples. Proteins enriched in amended soils were those potentially involved in the production of secondary metabolites/antibiotics, motility, keratin-degradation, and contractile secretion system proteins. We hypothesize these taxa contribute to the amendment-induced suppression effect due to their genomic potential to produce antibiotics, secrete effectors via the contractile secretion system, and degrade oxalate-a potential virulence factor of R. solani-while simultaneously possessing the ability to metabolize keratin.
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Affiliation(s)
- Lina Russ
- Wageningen Plant Research, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Beatriz Andreo Jimenez
- Wageningen Plant Research, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Els Nijhuis
- Wageningen Plant Research, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Joeke Postma
- Wageningen Plant Research, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Sun R, You R, Yu X, Zhao D, Li L. Discovery and Synthesis of a Gram-Negative-Active Cationic Lipopeptide Antibiotic Inspired by Primary Sequences from Underexplored Gram-Negative Bacteria. Org Lett 2024; 26:1348-1352. [PMID: 38341869 DOI: 10.1021/acs.orglett.3c04232] [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: 02/13/2024]
Abstract
The emergence of multidrug-resistant Gram-negative pathogens poses a serious threat to global health. Gram-negative bacteria have become increasingly recognized as underexplored sources of Gram-negative-active cationic lipopeptide (CLP) antibiotics. We systematically screened 8982 sequenced genomes from 42 underexplored Gram-negative bacterial genera and identified eight potential CLP biosynthetic gene clusters. Their predicted products were rapidly accessed by solid-phase total synthesis, which led to the novel antibiotic chospeptin with good activities against clinically isolated colistin-resistant Gram-negative pathogens.
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Affiliation(s)
- Runze Sun
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Ruixiang You
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai 200234, China
| | - Xuchang Yu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Di Zhao
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Lei Li
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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Hu Y, Yang X, Tai B, Wang G, Zhang X, Yin Y, Xing F. Bacillus amyloliquefaciens A-1 inhibiting fungal spoilage in agricultural products is improved by metabolic engineering of enhancing surfactin yield. Food Res Int 2024; 175:113752. [PMID: 38129052 DOI: 10.1016/j.foodres.2023.113752] [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: 07/25/2023] [Revised: 11/15/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
Fungi and subsequent mycotoxins contamination in agricultural products have caused enormous losses and great harm to human and animal health. Biological control has attracted the attention of researchers due to its advantages, including mild conditions, low cost, high efficiency and low nutrient loss. In this study, a newly isolated strain Bacillus amyloliquefaciens A-1 (A-1), was screened for its ability to inhibit the growth and Aflatoxin B1 (AFB1) production of Aspergillus flavus NRRL 3357. Electron microscopy results revealed that mycelium and conidia of A. flavus were destroyed by A-1, affecting hyphae, cell walls, cell membranes and organelles. RNA-seq analysis indicated disturbance in gene expression profiles of A. flavus, including amino acid degradation and starch and sucrose metabolism pathways. Importantly, the biosynthesis of AFB1 was significantly inhibited by the down-regulation of key regulatory genes, aflR and aflS, and the simultaneous down-regulation of most structural genes. Genome analysis predicted six secondary metabolites biosynthetic gene clusters. Then, four surfactin synthesized by cluster C were identified as the main active substance of A-1 using HPLC-Q-TOF-MS. The addition of alanine, threonine, Fe2+ increased surfactin production. Notably, the overexpression of comX also improved surfactin production. The vivo test results indicated that A-1 could significantly inhibit the decay of pear by Aspergillus westerdijkiae, and the mildew of maize and peanuts. Especially, the overexpression of comX in A-1 could enhance the inhibitory activity. In conclusion, the inhibition mechanism of A-1 was revealed, and comX was found can improve the production of surfactin and subsequent activities, which provides the scientific basis for the development of biocontrol agents to reduce spoilage in agricultural products.
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Affiliation(s)
- Yafan Hu
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs / Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Xu Yang
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs / Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Bowen Tai
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs / Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Gang Wang
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs / Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
| | - Xinlong Zhang
- Shandong Xinfurui Agricultural Science and Technology Co., Ltd. Liaocheng 252000, PR China
| | - Yixuan Yin
- Shandong Xinfurui Agricultural Science and Technology Co., Ltd. Liaocheng 252000, PR China
| | - Fuguo Xing
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs / Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
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Konkol D, Popiela E, Opaliński S, Lipińska A, Tymoszewski A, Krasowska A, Łukaszewicz M, Korczyński M. Effects of fermented rapeseed meal on performance, intestinal morphology, the viscosity of intestinal content, phosphorus availability, and egg quality of laying hens. Poult Sci 2024; 103:103256. [PMID: 37980734 PMCID: PMC10684812 DOI: 10.1016/j.psj.2023.103256] [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: 04/18/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/21/2023] Open
Abstract
Fermented rapeseed meal has the potential to partial replace soybean meal in feed mixtures for poultry without a negative impact on the health condition and performance of birds. This is due to the fact that the fermentation process can reduce the amount of antinutritional factors, improve the use of nutrients and impart probiotic properties to rapeseed meal. Therefore, this study was undertaken to investigate the effect of fermented rapeseed meal on the performance, egg quality, intestinal morphometry, the viscosity of intestinal content and total phosphorus availability. A total of 108 Lohmann Brown laying hens at 26 wk of age were used in the 90-day study. All hens were randomly divided into 3 treatment groups, with 12 replicates (cages) each, as follows: control group received no rapeseed meal, the URSM group received 3% unfermented rapeseed meal and the FRSM group received 3% fermented rapeseed meal. In the case of performance, egg traits, sensory evaluation of eggs, the viscosity of intestinal content and the availability of total phosphorus, if the distribution was normal, a 1-way analysis of variance was performed. If the distribution was not normal, the Kruskal-Wallis test was performed. In the case of histomorphometric evaluation of the intestine, if the distribution was normal, the Student t test for independent samples was performed. If not, a Mann-Whitney U test was performed. The performed analyses showed that the supplementation of fermented rapeseed meal had no negative effect on the performance of birds and the quality of eggs. Fermented rapeseed meal was also associated with improved histomorphometric parameters of the small intestine compared to the group receiving unfermented rapeseed meal in the feed. Laying hens from FRSM group were characterized by significantly lower viscosity of intestinal content (P < 0.05) compared to URSM group. Phosphorus in FRSM group was significantly more available to the birds (P < 0.05) compared to URSM group. These results suggest that supplementation with fermented rapeseed meal may be beneficial, especially in times of unstable prices of soybean meal and problems with its availability.
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Affiliation(s)
- Damian Konkol
- Department of Animal Nutrition and Feed Sciences, Wroclaw University of Environmental and Life Sciences, 51-630 Wrocław, Poland.
| | - Ewa Popiela
- Department of Environmental Hygiene and Animal Welfare, Wroclaw University of Environmental and Life Sciences, 51-630 Wrocław, Poland
| | - Sebastian Opaliński
- Department of Environmental Hygiene and Animal Welfare, Wroclaw University of Environmental and Life Sciences, 51-630 Wrocław, Poland
| | - Anna Lipińska
- Department of Animal Physiology and Biostructure, Wroclaw University of Environmental and Life Sciences, 50-375 Wrocław, Poland
| | - Adam Tymoszewski
- Chair of Drug and Cosmetics Biotechnology, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Anna Krasowska
- Department of Biotransformation, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Marcin Łukaszewicz
- Department of Biotransformation, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Mariusz Korczyński
- Department of Animal Nutrition and Feed Sciences, Wroclaw University of Environmental and Life Sciences, 51-630 Wrocław, Poland
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Zhang H, Xiu M, Li H, Li M, Xue X, He Y, Sun W, Yuan X, Liu Z, Li X, Merriman TR, Li C. Cadmium exposure dysregulates purine metabolism and homeostasis across the gut-liver axis in a mouse model. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 266:115587. [PMID: 37837700 DOI: 10.1016/j.ecoenv.2023.115587] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 10/16/2023]
Abstract
Cadmium (Cd) exposure has been associated with the development of enterohepatic circulation disorders and hyperuricemia, but the possible contribution of chronic low-dose Cd exposure to disease progression is still need to be explored. A mouse model of wild-type mice (WT) and Uox-knockout mice (Uox-KO) to find out the toxic effects of chronic low-dose Cd exposure on liver purine metabolism by liquid chromatography-mass spectrometry (LC-MS) platform and associated intestinal flora. High throughput omics analysis including metabolomics and transcriptomics showed that Cd exposure can cause disruption of purine metabolism and energy metabolism. Cd changes several metabolites associated with purine metabolism (xanthine, hypoxanthine, adenosine, uridine, inosine) and related genes, which are associated with elevated urate levels. Microbiome analysis showed that Cd exposure altered the disturbance of homeostasis in the gut. Uox-KO mice were more susceptible to Cd than WT mice. Our findings extend the understanding of potential toxicological interactions between liver and gut microbiota and shed light on the progression of metabolic diseases caused by Cd exposure.
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Affiliation(s)
- Hui Zhang
- Institute of Metabolic Diseases, Qingdao University, Qingdao, China; Shandong Provincial Key Laboratory of Metabolic Diseases and Qingdao Key Laboratory of Gout, the Affiliated Hospital of Qingdao University, Qingdao, China; Shandong Provincial Clinical Research Center for Immune Diseases and Gout, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Meng Xiu
- Plateau Atmosphere and Environment Key Laboratory of Sichuan Province, School of Atmospheric Sciences, Chengdu University of Information Technology, China
| | - Hailong Li
- Medical College, Binhai University, Qingdao, China
| | - Maichao Li
- Institute of Metabolic Diseases, Qingdao University, Qingdao, China; Shandong Provincial Key Laboratory of Metabolic Diseases and Qingdao Key Laboratory of Gout, the Affiliated Hospital of Qingdao University, Qingdao, China; Shandong Provincial Clinical Research Center for Immune Diseases and Gout, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaomei Xue
- Institute of Metabolic Diseases, Qingdao University, Qingdao, China; Shandong Provincial Key Laboratory of Metabolic Diseases and Qingdao Key Laboratory of Gout, the Affiliated Hospital of Qingdao University, Qingdao, China; Shandong Provincial Clinical Research Center for Immune Diseases and Gout, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yuwei He
- Institute of Metabolic Diseases, Qingdao University, Qingdao, China; Shandong Provincial Clinical Research Center for Immune Diseases and Gout, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wenyan Sun
- Institute of Metabolic Diseases, Qingdao University, Qingdao, China; Shandong Provincial Clinical Research Center for Immune Diseases and Gout, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xuan Yuan
- Institute of Metabolic Diseases, Qingdao University, Qingdao, China; Shandong Provincial Key Laboratory of Metabolic Diseases and Qingdao Key Laboratory of Gout, the Affiliated Hospital of Qingdao University, Qingdao, China; Shandong Provincial Clinical Research Center for Immune Diseases and Gout, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhen Liu
- Institute of Metabolic Diseases, Qingdao University, Qingdao, China; Shandong Provincial Clinical Research Center for Immune Diseases and Gout, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xinde Li
- Institute of Metabolic Diseases, Qingdao University, Qingdao, China; Shandong Provincial Clinical Research Center for Immune Diseases and Gout, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Tony R Merriman
- Institute of Metabolic Diseases, Qingdao University, Qingdao, China; Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, AL, United States
| | - Changgui Li
- Institute of Metabolic Diseases, Qingdao University, Qingdao, China; Shandong Provincial Key Laboratory of Metabolic Diseases and Qingdao Key Laboratory of Gout, the Affiliated Hospital of Qingdao University, Qingdao, China; Shandong Provincial Clinical Research Center for Immune Diseases and Gout, the Affiliated Hospital of Qingdao University, Qingdao, China.
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Pan X, Raaijmakers JM, Carrión VJ. Importance of Bacteroidetes in host-microbe interactions and ecosystem functioning. Trends Microbiol 2023; 31:959-971. [PMID: 37173204 DOI: 10.1016/j.tim.2023.03.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 05/15/2023]
Abstract
Bacteroidetes are prevalent in soil ecosystems and are associated with various eukaryotic hosts, including plants, animals, and humans. The ubiquity and diversity of Bacteroidetes exemplify their impressive versatility in niche adaptation and genomic plasticity. Over the past decade, a wealth of knowledge has been obtained on the metabolic functions of clinically relevant Bacteroidetes, but much less attention has been given to Bacteroidetes living in close association with plants. To improve our understanding of the functional roles of Bacteroidetes for plants and other hosts, we review the current knowledge of their taxonomy and ecology, in particular their roles in nutrient cycling and host fitness. We highlight their environmental distribution, stress resilience, genomic diversity, and functional importance in diverse ecosystems, including, but not limited to, plant-associated microbiomes.
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Affiliation(s)
- Xinya Pan
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands; Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain; Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Málaga, Spain.
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Kim DY, Han JW, Lee JW, Kim B, Kim YS, Kim HT, Choi GJ, Kim H. Biocontrol potential of Chitinophaga flava HK235 producing antifungal-related peptide chitinocin. Front Microbiol 2023; 14:1170673. [PMID: 37283917 PMCID: PMC10239826 DOI: 10.3389/fmicb.2023.1170673] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/05/2023] [Indexed: 06/08/2023] Open
Abstract
Botrytis cinerea is a necrotrophic fungal pathogen with an extremely broad host range, causing significant economic losses in agricultural production. In this study, we discovered a culture filtrate of bacterial strain HK235, which was identified as Chitinophaga flava, exhibiting high levels of antifungal activity against B. cinerea. From the HK235 culture filtrate, we isolated a new antimicrobial peptide molecule designated as chitinocin based on activity-guided fractionation followed by characterization of the amino acid composition and spectroscopic analyses. The HK235 culture filtrate and chitinocin completely inhibited both conidial germination and mycelial growth of B. cinerea at a concentration of 20% and 200 μg/mL, respectively. In addition to antibiosis against B. cinerea, the active compound chitinocin had a broad antifungal and antibacterial activity in vitro. When tomato plants were treated with the culture filtrate and chitinocin, the treatment strongly reduced the development of gray mold disease in a concentration-dependent manner compared to the untreated control. Here, considering the potent antifungal property in vitro and in vivo, we present the biocontrol potential of C. flava HK235 for the first time.
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Affiliation(s)
- Da Yeon Kim
- Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, South Korea
- Department of Plant Medicine, Chungbuk National University, Cheongju, South Korea
| | - Jae Woo Han
- Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, South Korea
| | - Jin Woo Lee
- Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, South Korea
- Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, South Korea
| | - Bomin Kim
- Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, South Korea
- Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, South Korea
| | - Yeong Seok Kim
- Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, South Korea
- Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, South Korea
| | - Heung-Tae Kim
- Department of Plant Medicine, Chungbuk National University, Cheongju, South Korea
| | - Gyung Ja Choi
- Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, South Korea
- Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, South Korea
| | - Hun Kim
- Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, South Korea
- Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, South Korea
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10
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Riyanti, Zumkeller CM, Spohn M, Mihajlovic S, Schwengers O, Goesmann A, Choironi NA, Schäberle TF, Harwoko H. Draft Genome Sequences of Algoriphagus sp. Strain PAP.12 and Roseivirga sp. Strain PAP.19, Isolated from Marine Samples from Papua, Indonesia. Microbiol Resour Announc 2023; 12:e0126422. [PMID: 36927116 PMCID: PMC10112063 DOI: 10.1128/mra.01264-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/22/2023] [Indexed: 03/18/2023] Open
Abstract
Algoriphagus sp. strain PAP.12 (EXT111900) and Roseivirga sp. strain PAP.19 (EXT111901) were isolated from marine samples. Here, we report their draft genome sequences, 5.032 Mbp and 4.583 Mbp in size, respectively, and rate their specialized metabolite production capacity. Taxonomic ranks established by genome-based analysis indicate that Algoriphagus sp. strain PAP.12 represents a candidate new species.
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Affiliation(s)
- Riyanti
- Faculty of Fisheries and Marine Science, Jenderal Soedirman University, Purwokerto, Indonesia
| | - Celine M. Zumkeller
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Marius Spohn
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | - Sanja Mihajlovic
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Oliver Schwengers
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Nur A. Choironi
- Department of Pharmacy, Faculty of Health Sciences, Jenderal Soedirman University, Purwokerto, Indonesia
| | - Till F. Schäberle
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Giessen, Germany
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | - Harwoko Harwoko
- Department of Pharmacy, Faculty of Health Sciences, Jenderal Soedirman University, Purwokerto, Indonesia
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11
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Riyanti, Zumkeller CM, Spohn M, Mihajlovic S, Schwengers O, Goesmann A, Riviani R, Meinita MDN, Schäberle TF, Harwoko H. Draft Genome Sequence of Sinomicrobium sp. Strain PAP.21, Isolated from a Coast Sample of Papua, Indonesia. Microbiol Resour Announc 2023; 12:e0126822. [PMID: 36943053 PMCID: PMC10112250 DOI: 10.1128/mra.01268-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
Sinomicrobium sp. strain PAP.21 (EXT111902) was isolated from the coast of Cenderawasih Bay National Park in West Papua, Indonesia. Its genome was assembled into 151 contigs with a total size of 5.439 Mbp, enabling the prediction of its specialized metabolite production capacity.
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Affiliation(s)
- Riyanti
- Faculty of Fisheries and Marine Science, Jenderal Soedirman University, Purwokerto, Indonesia
| | - Celine M Zumkeller
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Marius Spohn
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | - Sanja Mihajlovic
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Oliver Schwengers
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Riviani Riviani
- Faculty of Fisheries and Marine Science, Jenderal Soedirman University, Purwokerto, Indonesia
| | - Maria D N Meinita
- Faculty of Fisheries and Marine Science, Jenderal Soedirman University, Purwokerto, Indonesia
| | - Till F Schäberle
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | - Harwoko Harwoko
- Department of Pharmacy, Faculty of Health Sciences, Jenderal Soedirman University, Purwokerto, Indonesia
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12
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Marner M, Kolberg L, Horst J, Böhringer N, Hübner J, Kresna IDM, Liu Y, Mettal U, Wang L, Meyer-Bühn M, Mihajlovic S, Kappler M, Schäberle TF, von Both U. Antimicrobial Activity of Ceftazidime-Avibactam, Ceftolozane-Tazobactam, Cefiderocol, and Novel Darobactin Analogs against Multidrug-Resistant Pseudomonas aeruginosa Isolates from Pediatric and Adolescent Cystic Fibrosis Patients. Microbiol Spectr 2023; 11:e0443722. [PMID: 36692293 PMCID: PMC9927382 DOI: 10.1128/spectrum.04437-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/02/2023] [Indexed: 01/25/2023] Open
Abstract
The emergence and spread of antimicrobial resistance (AMR) in Gram-negative pathogens, such as carbapenem-resistant Pseudomonas aeruginosa, pose an increasing threat to health care. Patients with immunodeficiencies or chronic pulmonary disease, like cystic fibrosis (CF), are particularly vulnerable to Pseudomonas infections and depend heavily on antibiotic therapy. To broaden limited treatment options, this study evaluated the potency of the recently licensed drugs ceftazidime-avibactam (CZA), ceftolozane-tazobactam (C/T), and cefiderocol (FDC) as well as two novel preclinical antibiotics, darobactins B (DAR B) and B9 (DAR B9), against clinical P. aeruginosa isolates derived from respiratory samples of CF patients. We observed high levels of resistance to all three newly licensed drugs, with cefiderocol exhibiting the best activity. From the 66 investigated P. aeruginosa isolates, a total of 53% were resistant to CZA, 49% to C/T, and 30% to FDC. Strikingly, 52 of the evaluated isolates were obtained from CF patients prior to market introduction of the drugs. Thus, our results suggest that resistance to CZA, C/T, and FDC may be due to preexisting resistance mechanisms. On the other hand, our two novel preclinical compounds performed better than (CZA and C/T) or close to (FDC) the licensed drugs-most likely due to the novel mode of action. Thus, our results highlight the necessity of global consistency in the area of antibiotic stewardship to prevent AMR from further impairing the potency of antibiotics in clinical practice. Ultimately, this study demonstrates the urgency to support the development of novel antimicrobials, preferably with a new mode of action such as darobactins B and B9, two very promising antimicrobial compounds for the treatment of critically ill patients suffering from multidrug-resistant Gram-negative (MRGN) infections. IMPORTANCE Antimicrobial resistance (AMR) represents an ever increasing threat to the health care system. Even recently licensed drugs are often not efficient for the treatment of infections caused by Gram-negative bacteria, like Pseudomonas aeruginosa, a causative agent of lung infections. To address this unmet medical need, innovative antibiotics, which possess a new mode of action, need to be developed. Here, the antibiogram of clinical isolates derived from cystic fibrosis patients was generated and new bicyclic heptapeptides, which inhibit the outer membrane protein BamA, exhibited strong activity, also against multidrug-resistant isolates.
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Affiliation(s)
- Michael Marner
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
- Justus-Liebig-University of Giessen, Giessen, Germany
| | - Laura Kolberg
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Julia Horst
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
- Institute for Medical Information Processing, Biometry, and Epidemiology – IBE, LMU Munich, Munich, Germany
- Pettenkofer School of Public Health, Munich, Germany
| | - Nils Böhringer
- Justus-Liebig-University of Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Johannes Hübner
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | | | - Yang Liu
- Justus-Liebig-University of Giessen, Giessen, Germany
| | - Ute Mettal
- Justus-Liebig-University of Giessen, Giessen, Germany
| | - Lei Wang
- Justus-Liebig-University of Giessen, Giessen, Germany
| | - Melanie Meyer-Bühn
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Sanja Mihajlovic
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
| | - Matthias Kappler
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Till F. Schäberle
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
- Justus-Liebig-University of Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Ulrich von Both
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
- Pettenkofer School of Public Health, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
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13
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Song Y, Sun L, Zhang S, Fan K, Wang H, Shi Y, Shen Y, Wang W, Zhang J, Han X, Mao Y, Wang Y, Ding Z. Enzymes and microorganisms jointly promote the fermentation of rapeseed cake. Front Nutr 2022; 9:989410. [PMID: 36185678 PMCID: PMC9521174 DOI: 10.3389/fnut.2022.989410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/18/2022] [Indexed: 11/25/2022] Open
Abstract
Rapeseed cake is a by-product of rapeseed oil separation. The nutritional components of rapeseed cake mainly include a variety of carbohydrates, proteins, and minerals. In order to improve the conversion rate of rapeseed cake, we studied the physicochemical properties, the structure of microbial communities, and the composition of metabolites in rapeseed cake after enzymatic fermentation. The results showed that the addition of enzymatic preparation increased microbial diversity. The relative abundance of Bacillus, Lysinibacillus, Empedobacter, Debaryomyces, Hyphopichia, and Komagataella in enzymatic fermentation was significantly higher than that in natural fermentation. Unlike natural fermentation, microbial diversity during enzymatic fermentation is specific, which improves the efficiency of fermentation. Otherwise, enzymatic fermentation promotes the conversion of macromolecular substances in rapeseed cake, which increases small metabolites, such as fatty acids, organic acids, amino acids and their derivatives. The metabolite enrichment pathway is mostly concentrated in sugar metabolism and fatty acid metabolism. In conclusion, after adding enzymatic preparation, enzymes and microorganisms jointly promote the transformation of macromolecules during the fermentation of rapeseed cake, which laid a good foundation for further utilization of rapeseed cake.
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Affiliation(s)
- Yujie Song
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Litao Sun
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Shuning Zhang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Kai Fan
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Huan Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Yujie Shi
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Yaozong Shen
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Wenmei Wang
- Co-construction Service Center of Three Districts in Taolin Town, Shandong, China
| | - Jie Zhang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Xiao Han
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Yilin Mao
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
- *Correspondence: Yu Wang,
| | - Zhaotang Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Zhaotang Ding,
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