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Kothe CI, Carøe C, Mazel F, Zilber D, Cruz-Morales P, Mohellibi N, Evans JD. Novel misos shape distinct microbial ecologies: opportunities for flavourful sustainable food innovation. Food Res Int 2024; 189:114490. [PMID: 38876584 DOI: 10.1016/j.foodres.2024.114490] [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: 02/28/2024] [Revised: 04/30/2024] [Accepted: 05/07/2024] [Indexed: 06/16/2024]
Abstract
Fermentation is resurgent around the world as people seek healthier, more sustainable, and tasty food options. This study explores the microbial ecology of miso, a traditional Japanese fermented paste, made with novel regional substrates to develop new plant-based foods. Eight novel miso varieties were developed using different protein-rich substrates: yellow peas, Gotland lentils, and fava beans (each with two treatments: standard and nixtamalisation), as well as rye bread and soybeans. The misos were produced at Noma, a restaurant in Copenhagen, Denmark. Samples were analysed with biological and technical triplicates at the beginning and end of fermentation. We also incorporated in this study six samples of novel misos produced following the same recipe at Inua, a former affiliate restaurant of Noma in Tokyo, Japan. To analyse microbial community structure and diversity, metabarcoding (16S and ITS) and shotgun metagenomic analyses were performed. The misos contain a greater range of microbes than is currently described for miso in the literature. The composition of the novel yellow pea misos was notably similar to the traditional soybean ones, suggesting they are a good alternative, which supports our culinary collaborators' sensory conclusions. For bacteria, we found that overall substrate had the strongest effect, followed by time, treatment (nixtamalisation), and geography. For fungi, there was a slightly stronger effect of geography and a mild effect of substrate, and no significant effects for treatment or time. Based on an analysis of metagenome-assembled genomes (MAGs), strains of Staphylococccus epidermidis differentiated according to substrate. Carotenoid biosynthesis genes in these MAGs appeared in strains from Japan but not from Denmark, suggesting a possible gene-level geographical effect. The benign and possibly functional presence of S. epidermidis in these misos, a species typically associated with the human skin microbiome, suggests possible adaptation to the miso niche, and the flow of microbes between bodies and foods in certain fermentation as more common than is currently recognised. This study improves our understanding of miso ecology, highlights the potential for developing novel misos using diverse local ingredients, and suggests how fermentation innovation can contribute to studies of microbial ecology and evolution.
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Affiliation(s)
- Caroline Isabel Kothe
- Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark.
| | | | - Florent Mazel
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
| | - David Zilber
- Novonesis, Hørsholm, Denmark; Restaurant Noma, Copenhagen, Denmark
| | - Pablo Cruz-Morales
- Yeast Natural Products, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Nacer Mohellibi
- Université Paris-Saclay, INRAE, Micalis Institute, Jouy-en-Josas, France
| | - Joshua D Evans
- Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark.
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Alexa EA, Cobo-Díaz JF, Renes E, O Callaghan TF, Kilcawley K, Mannion D, Skibinska I, Ruiz L, Margolles A, Fernández-Gómez P, Alvarez-Molina A, Puente-Gómez P, Crispie F, López M, Prieto M, Cotter PD, Alvarez-Ordóñez A. The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits. MICROBIOME 2024; 12:78. [PMID: 38678226 PMCID: PMC11055350 DOI: 10.1186/s40168-024-01790-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/08/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND Artisanal cheeses usually contain a highly diverse microbial community which can significantly impact their quality and safety. Here, we describe a detailed longitudinal study assessing the impact of ripening in three natural caves on the microbiome and resistome succession across three different producers of Cabrales blue-veined cheese. RESULTS Both the producer and cave in which cheeses were ripened significantly influenced the cheese microbiome. Lactococcus and the former Lactobacillus genus, among other taxa, showed high abundance in cheeses at initial stages of ripening, either coming from the raw material, starter culture used, and/or the environment of processing plants. Along cheese ripening in caves, these taxa were displaced by other bacteria, such as Tetragenococcus, Corynebacterium, Brevibacterium, Yaniella, and Staphylococcus, predominantly originating from cave environments (mainly food contact surfaces), as demonstrated by source-tracking analysis, strain analysis at read level, and the characterization of 613 metagenome-assembled genomes. The high abundance of Tetragenococcus koreensis and Tetragenococcus halophilus detected in cheese has not been found previously in cheese metagenomes. Furthermore, Tetragenococcus showed a high level of horizontal gene transfer with other members of the cheese microbiome, mainly with Lactococcus and Staphylococcus, involving genes related to carbohydrate metabolism functions. The resistome analysis revealed that raw milk and the associated processing environments are a rich reservoir of antimicrobial resistance determinants, mainly associated with resistance to aminoglycosides, tetracyclines, and β-lactam antibiotics and harbored by aerobic gram-negative bacteria of high relevance from a safety point of view, such as Escherichia coli, Salmonella enterica, Acinetobacter, and Klebsiella pneumoniae, and that the displacement of most raw milk-associated taxa by cave-associated taxa during ripening gave rise to a significant decrease in the load of ARGs and, therefore, to a safer end product. CONCLUSION Overall, the cave environments represented an important source of non-starter microorganisms which may play a relevant role in the quality and safety of the end products. Among them, we have identified novel taxa and taxa not previously regarded as being dominant components of the cheese microbiome (Tetragenococcus spp.), providing very valuable information for the authentication of this protected designation of origin artisanal cheese. Video Abstract.
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Affiliation(s)
- Elena A Alexa
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Erica Renes
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Tom F O Callaghan
- School of Food and Nutritional Sciences, University College Cork, Cork, T12 Y337, Ireland
| | | | - David Mannion
- Teagasc Food Research Centre, Fermoy, Co., Cork, Ireland
| | | | - Lorena Ruiz
- Dairy Research Institute, Spanish National Research Council, Instituto de Productos Lácteos de Asturias-CSIC, Villaviciosa, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011, Oviedo, Asturias, Spain
| | - Abelardo Margolles
- Dairy Research Institute, Spanish National Research Council, Instituto de Productos Lácteos de Asturias-CSIC, Villaviciosa, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011, Oviedo, Asturias, Spain
| | | | | | - Paula Puente-Gómez
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Fiona Crispie
- Teagasc Food Research Centre, Fermoy, Co., Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Mercedes López
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Miguel Prieto
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Paul D Cotter
- Teagasc Food Research Centre, Fermoy, Co., Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- VistaMilk, Cork, Ireland
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology, Universidad de León, León, Spain.
- Institute of Food Science and Technology, Universidad de León, León, Spain.
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3
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Reuben RC, Torres C. Bacteriocins: potentials and prospects in health and agrifood systems. Arch Microbiol 2024; 206:233. [PMID: 38662051 PMCID: PMC11045635 DOI: 10.1007/s00203-024-03948-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024]
Abstract
Bacteriocins are highly diverse, abundant, and heterogeneous antimicrobial peptides that are ribosomally synthesized by bacteria and archaea. Since their discovery about a century ago, there has been a growing interest in bacteriocin research and applications. This is mainly due to their high antimicrobial properties, narrow or broad spectrum of activity, specificity, low cytotoxicity, and stability. Though initially used to improve food quality and safety, bacteriocins are now globally exploited for innovative applications in human, animal, and food systems as sustainable alternatives to antibiotics. Bacteriocins have the potential to beneficially modulate microbiota, providing viable microbiome-based solutions for the treatment, management, and non-invasive bio-diagnosis of infectious and non-infectious diseases. The use of bacteriocins holds great promise in the modulation of food microbiomes, antimicrobial food packaging, bio-sanitizers and antibiofilm, pre/post-harvest biocontrol, functional food, growth promotion, and sustainable aquaculture. This can undoubtedly improve food security, safety, and quality globally. This review highlights the current trends in bacteriocin research, especially the increasing research outputs and funding, which we believe may proportionate the soaring global interest in bacteriocins. The use of cutting-edge technologies, such as bioengineering, can further enhance the exploitation of bacteriocins for innovative applications in human, animal, and food systems.
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Affiliation(s)
- Rine Christopher Reuben
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain.
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain
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Fang GY, Liu XQ, Jiang YJ, Mu XJ, Huang BW. Horizontal gene transfer in activated sludge enhances microbial antimicrobial resistance and virulence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168908. [PMID: 38013098 DOI: 10.1016/j.scitotenv.2023.168908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
Activated sludge (AS) plays a vital role in removing organic pollutants and nutrients from wastewater. However, the risks posed by horizontal gene transfer (HGT) between bacteria in AS are still unclear. Here, a total of 478 high-quality non-redundant metagenome-assembled genomes (MAGs) were obtained. >50 % and 5 % of MAGs were involved in at least one HGT and recent HGT, respectively. Most of the transfers (82.4 %) of antimicrobial resistance genes (ARGs) occurred among the classes of Alphaproteobacteria and Gammaproteobacteria. The bacteria involved in the transfers of virulence factor genes (VFGs) mainly include Alphaproteobacteria (42.3 %), Bacteroidia (19.2 %), and Gammaproteobacteria (11.5 %). Moreover, the number of ARGs and VFGs in the classes of Alphaproteobacteria and Gammaproteobacteria was higher than that in other bacteria (P < 0.001). Mobile genetic elements were important contributors to ARGs and VFGs in AS bacteria. These results have implications for the management of antimicrobial resistance and virulence in activated sludge microorganisms.
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Affiliation(s)
- Guan-Yu Fang
- College of Food and Health, Zhejiang A&F University, Hangzhou 311300, PR China; National Grain Industry (High-Quality Rice Storage in Temperate and Humid Region) Technology Innovation Center, Zhejiang A&F University, Hangzhou 311300, PR China.
| | - Xing-Quan Liu
- College of Food and Health, Zhejiang A&F University, Hangzhou 311300, PR China; National Grain Industry (High-Quality Rice Storage in Temperate and Humid Region) Technology Innovation Center, Zhejiang A&F University, Hangzhou 311300, PR China
| | - Yu-Jian Jiang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, PR China
| | - Xiao-Jing Mu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, PR China
| | - Bing-Wen Huang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, PR China
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5
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Schuetz R, Claypool J, Sfriso R, Vollhardt JH. Sunscreens can preserve human skin microbiome upon erythemal UV exposure. Int J Cosmet Sci 2024; 46:71-84. [PMID: 37664974 DOI: 10.1111/ics.12910] [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: 04/05/2023] [Revised: 08/09/2023] [Accepted: 08/23/2023] [Indexed: 09/05/2023]
Abstract
OBJECTIVE Ultraviolet radiation (UVR) is a known environmental key factor for premature skin ageing. Only few scientific evidence is available to support the effects of UVR on the skin microbiome. This in vivo pilot study aimed to evaluate the impact on the skin microbiome upon erythemal UV exposure and the protection of UV-exposed skin microbiome by UV filters. METHODS Ten female volunteers were treated with an sun protection factor (SPF) 20 sunscreen and placebo formulation (without UV filters) on their upper middle backs and irradiated with an erythemal dose (2 MED) by a solar simulator. Skin swabbing samples from four zones (i.e., unexposed, exposed, sunscreen- and placebo-treated on exposed skin) were collected for the microbiome analysis before and 2 h after UV exposure, respectively, and processed via shallow 16S rRNA Amplicon and Shotgun metagenomic sequencing. An in vitro UV method was developed to confirm the protection of isolated bacterial strains by single UV filters and combinations. RESULTS Alpha diversity was impacted by significant inter-individual differences and by treatment rather than by irradiation. Cutibacterium acnes was found to be the most abundant and a confounding factor for diversity. On a species level, Lactobacillus crispatus was negatively associated with UVR and placebo treatment, whereas there was a positive association with sunscreen treatment. The sunscreen treatment also favoured an interaction network with central Micrococcus genus. The in vitro results showed that both single UV filters and combinations had specific effects on the survival rates of L. crispatus, C. acnes, and Staphylococcus epidermidis. CONCLUSION We identified potential microorganisms and bacterial interactions that were associated with an SPF 20 sunscreen treatment. The specific protection of L. crispatus as a key player in the UV-exposed skin microbiome and reduction of C. acnes population by UV filters might lead to new cosmetic concepts for photoprotection.
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Affiliation(s)
- Rolf Schuetz
- Personal Care and Aroma, DSM Nutritional Products Ltd, Kaiseraugst, Switzerland
| | - Joshua Claypool
- Biodata and Translation, DSM Nutritional Products, Lexington, Massachusetts, USA
| | - Riccardo Sfriso
- Personal Care and Aroma, DSM Nutritional Products Ltd, Kaiseraugst, Switzerland
| | - Juergen H Vollhardt
- Personal Care and Aroma, DSM Nutritional Products Ltd, Kaiseraugst, Switzerland
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Lan F, Saba J, Ross TD, Zhou Z, Krauska K, Anantharaman K, Landick R, Venturelli OS. Massively parallel single-cell sequencing of diverse microbial populations. Nat Methods 2024; 21:228-235. [PMID: 38233503 PMCID: PMC11089590 DOI: 10.1038/s41592-023-02157-7] [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: 04/24/2022] [Accepted: 12/17/2023] [Indexed: 01/19/2024]
Abstract
Single-cell genetic heterogeneity is ubiquitous in microbial populations and an important aspect of microbial biology; however, we lack a broadly applicable and accessible method to study this heterogeneity in microbial populations. Here, we show a simple, robust and generalizable method for high-throughput single-cell sequencing of target genetic loci in diverse microbes using simple droplet microfluidics devices (droplet targeted amplicon sequencing; DoTA-seq). DoTA-seq serves as a platform to perform diverse assays for single-cell genetic analysis of microbial populations. Using DoTA-seq, we demonstrate the ability to simultaneously track the prevalence and taxonomic associations of >10 antibiotic-resistance genes and plasmids within human and mouse gut microbial communities. This workflow is a powerful and accessible platform for high-throughput single-cell sequencing of diverse microbial populations.
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Affiliation(s)
- Freeman Lan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Jason Saba
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Tyler D Ross
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Zhichao Zhou
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Katie Krauska
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA.
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Zhu S, Hong J, Wang T. Horizontal gene transfer is predicted to overcome the diversity limit of competing microbial species. Nat Commun 2024; 15:800. [PMID: 38280843 PMCID: PMC10821886 DOI: 10.1038/s41467-024-45154-w] [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: 07/23/2023] [Accepted: 01/17/2024] [Indexed: 01/29/2024] Open
Abstract
Natural microbial ecosystems harbor substantial diversity of competing species. Explaining such diversity is challenging, because in classic theories it is extremely infeasible for a large community of competing species to stably coexist in homogeneous environments. One important aspect mostly overlooked in these theories, however, is that microbes commonly share genetic materials with their neighbors through horizontal gene transfer (HGT), which enables the dynamic change of species growth rates due to the fitness effects of the mobile genetic elements (MGEs). Here, we establish a framework of species competition by accounting for the dynamic gene flow among competing microbes. Combining theoretical derivation and numerical simulations, we show that in many conditions HGT can surprisingly overcome the biodiversity limit predicted by the classic model and allow the coexistence of many competitors, by enabling dynamic neutrality of competing species. In contrast with the static neutrality proposed by previous theories, the diversity maintained by HGT is highly stable against random perturbations of microbial fitness. Our work highlights the importance of considering gene flow when addressing fundamental ecological questions in the world of microbes and has broad implications for the design and engineering of complex microbial consortia.
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Affiliation(s)
- Shiben Zhu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Juken Hong
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Teng Wang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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8
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You L, Jin H, Kwok LY, Lv R, Zhao Z, Bilige M, Sun Z, Liu W, Zhang H. Intraspecific microdiversity and ecological drivers of lactic acid bacteria in naturally fermented milk ecosystem. Sci Bull (Beijing) 2023; 68:2405-2417. [PMID: 37718237 DOI: 10.1016/j.scib.2023.09.001] [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] [Received: 03/20/2023] [Revised: 05/31/2023] [Accepted: 08/31/2023] [Indexed: 09/19/2023]
Abstract
Traditional fermented milks are produced by inoculating technique, which selects well-adapted microorganisms that have been passed on through generations. Few reports have used naturally fermented milks as model ecosystems to investigate the mechanism of formation of intra-species microbial diversity. Here, we isolated and whole-genome-sequenced a total of 717 lactic acid bacterial isolates obtained from 12 independent naturally fermented milks collect from 12 regions across five countries. We further analyzed the within-sample intra-species phylogenies of 214 Lactobacillus helveticus isolates, 97 Lactococcus lactis subsp. lactis isolates, and 325 Lactobacillus delbrueckii subsp. bulgaricus isolates. We observed a high degree of intra-species genomic and functional gene diversity within-/between-sample(s). Single nucleotide polymorphism-based phylogenetic reconstruction revealed great within-sample intra-species heterogeneity, evolving from multiple lineages. Further phylogenetic reconstruction (presence-absence gene profile) revealed within-sample inter-clade functional diversity (based on carbohydrate-active enzyme- and peptidase-encoding genes) in all three investigated species/subspecies. By identifying and mapping clade-specific genes of intra-sample clades of the three species/subspecies to the respective fermented milk metagenome, we found extensive potential inter-/intra-species horizontal gene transfer events. Finally, the microbial composition of the samples is closely linked to the nucleotide diversity of the respective species/subspecies. Overall, our results contribute to the conservation of lactic acid bacteria resources, providing ecological insights into the microbial ecosystem of naturally fermented dairy products.
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Affiliation(s)
- Lijun You
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Hao Jin
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lai-Yu Kwok
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Ruirui Lv
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Zhixin Zhao
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Menghe Bilige
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Zhihong Sun
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Wenjun Liu
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China.
| | - Heping Zhang
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China.
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Cumsille A, Serna-Cardona N, González V, Claverías F, Undabarrena A, Molina V, Salvà-Serra F, Moore ERB, Cámara B. Exploring the biosynthetic gene clusters in Brevibacterium: a comparative genomic analysis of diversity and distribution. BMC Genomics 2023; 24:622. [PMID: 37858045 PMCID: PMC10588199 DOI: 10.1186/s12864-023-09694-7] [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: 06/11/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Exploring Brevibacterium strains from various ecosystems may lead to the discovery of new antibiotic-producing strains. Brevibacterium sp. H-BE7, a strain isolated from marine sediments from Northern Patagonia, Chile, had its genome sequenced to study the biosynthetic potential to produce novel natural products within the Brevibacterium genus. The genome sequences of 98 Brevibacterium strains, including strain H-BE7, were selected for a genomic analysis. A phylogenomic cladogram was generated, which divided the Brevibacterium strains into four major clades. A total of 25 strains are potentially unique new species according to Average Nucleotide Identity (ANIb) values. These strains were isolated from various environments, emphasizing the importance of exploring diverse ecosystems to discover the full diversity of Brevibacterium. Pangenome analysis of Brevibacterium strains revealed that only 2.5% of gene clusters are included within the core genome, and most gene clusters occur either as singletons or as cloud genes present in less than ten strains. Brevibacterium strains from various phylogenomic clades exhibit diverse BGCs. Specific groups of BGCs show clade-specific distribution patterns, such as siderophore BGCs and carotenoid-related BGCs. A group of clade IV-A Brevibacterium strains possess a clade-specific Polyketide synthase (PKS) BGCs that connects with phenazine-related BGCs. Within the PKS BGC, five genes, including the biosynthetic PKS gene, participate in the mevalonate pathway and exhibit similarities with the phenazine A BGC. However, additional core biosynthetic phenazine genes were exclusively discovered in nine Brevibacterium strains, primarily isolated from cheese. Evaluating the antibacterial activity of strain H-BE7, it exhibited antimicrobial activity against Salmonella enterica and Listeria monocytogenes. Chemical dereplication identified bioactive compounds, such as 1-methoxyphenazine in the crude extracts of strain H-BE7, which could be responsible of the observed antibacterial activity. While strain H-BE7 lacks the core phenazine biosynthetic genes, it produces 1-methoxyphenazine, indicating the presence of an unknown biosynthetic pathway for this compound. This suggests the existence of alternative biosynthetic pathways or promiscuous enzymes within H-BE7's genome.
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Affiliation(s)
- Andrés Cumsille
- Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Néstor Serna-Cardona
- Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Valentina González
- Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Fernanda Claverías
- Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Agustina Undabarrena
- Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Vania Molina
- Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Francisco Salvà-Serra
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Region Västra Götaland and Sahlgrenska Academy, Culture Collection University of Gothenburg (CCUG), Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Edward R B Moore
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Region Västra Götaland and Sahlgrenska Academy, Culture Collection University of Gothenburg (CCUG), Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Beatriz Cámara
- Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile.
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10
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Walsh AM, Leech J, Huttenhower C, Delhomme-Nguyen H, Crispie F, Chervaux C, Cotter P. Integrated molecular approaches for fermented food microbiome research. FEMS Microbiol Rev 2023; 47:fuad001. [PMID: 36725208 PMCID: PMC10002906 DOI: 10.1093/femsre/fuad001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 12/28/2022] [Accepted: 01/09/2023] [Indexed: 02/03/2023] Open
Abstract
Molecular technologies, including high-throughput sequencing, have expanded our perception of the microbial world. Unprecedented insights into the composition and function of microbial communities have generated large interest, with numerous landmark studies published in recent years relating the important roles of microbiomes and the environment-especially diet and nutrition-in human, animal, and global health. As such, food microbiomes represent an important cross-over between the environment and host. This is especially true of fermented food microbiomes, which actively introduce microbial metabolites and, to a lesser extent, live microbes into the human gut. Here, we discuss the history of fermented foods, and examine how molecular approaches have advanced research of these fermented foods over the past decade. We highlight how various molecular approaches have helped us to understand the ways in which microbes shape the qualities of these products, and we summarize the impacts of consuming fermented foods on the gut. Finally, we explore how advances in bioinformatics could be leveraged to enhance our understanding of fermented foods. This review highlights how integrated molecular approaches are changing our understanding of the microbial communities associated with food fermentation, the creation of unique food products, and their influences on the human microbiome and health.
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Affiliation(s)
- Aaron M Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork and APC Microbiome Ireland, P61 C996, Ireland
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - John Leech
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork and APC Microbiome Ireland, P61 C996, Ireland
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork and APC Microbiome Ireland, P61 C996, Ireland
| | - Christian Chervaux
- Danone Nutricia Research, Centre Daniel Carasso, Palaiseau 91120, France
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork and APC Microbiome Ireland, P61 C996, Ireland
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11
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Plasmid-Encoded Traits Vary across Environments. mBio 2023; 14:e0319122. [PMID: 36629415 PMCID: PMC9973032 DOI: 10.1128/mbio.03191-22] [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] [Indexed: 01/12/2023] Open
Abstract
Plasmids are key mobile genetic elements in bacterial evolution and ecology as they allow the rapid adaptation of bacteria under selective environmental changes. However, the genetic information associated with plasmids is usually considered separately from information about their environmental origin. To broadly understand what kinds of traits may become mobilized by plasmids in different environments, we analyzed the properties and accessory traits of 9,725 unique plasmid sequences from a publicly available database with known bacterial hosts and isolation sources. Although most plasmid research focuses on resistance traits, such genes made up <1% of the total genetic information carried by plasmids. Similar to traits encoded on the bacterial chromosome, plasmid accessory trait compositions (including general Clusters of Orthologous Genes [COG] functions, resistance genes, and carbon and nitrogen genes) varied across seven broadly defined environment types (human, animal, wastewater, plant, soil, marine, and freshwater). Despite their potential for horizontal gene transfer, plasmid traits strongly varied with their host's taxonomic assignment. However, the trait differences across environments of broad COG categories could not be entirely explained by plasmid host taxonomy, suggesting that environmental selection acts on the plasmid traits themselves. Finally, some plasmid traits and environments (e.g., resistance genes in human-related environments) were more often associated with mobilizable plasmids (those having at least one detected relaxase) than others. Overall, these findings underscore the high level of diversity of traits encoded by plasmids and provide a baseline to investigate the potential of plasmids to serve as reservoirs of adaptive traits for microbial communities. IMPORTANCE Plasmids are well known for their role in the transmission of antibiotic resistance-conferring genes. Beyond human and clinical settings, however, they disseminate many other types of genes, including those that contribute to microbially driven ecosystem processes. In this study, we identified the distribution of traits genetically encoded by plasmids isolated from seven broadly categorized environments. We find that plasmid trait content varied with both bacterial host taxonomy and environment and that, on average, half of the plasmids were potentially mobilizable. As anthropogenic activities impact ecosystems and the climate, investigating and identifying the mechanisms of how microbial communities can adapt will be imperative for predicting the impacts on ecosystem functioning.
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12
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Longitudinal, Multi-Platform Metagenomics Yields a High-Quality Genomic Catalog and Guides an In Vitro Model for Cheese Communities. mSystems 2023; 8:e0070122. [PMID: 36622155 PMCID: PMC9948695 DOI: 10.1128/msystems.00701-22] [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] [Indexed: 01/10/2023] Open
Abstract
Microbiomes are intricately intertwined with human health, geochemical cycles, and food production. While many microbiomes of interest are highly complex and experimentally intractable, cheese rind microbiomes have proven to be powerful model systems for the study of microbial interactions. To provide a more comprehensive view of the genomic potential and temporal dynamics of cheese rind communities, we combined longitudinal, multi-platform metagenomics of three ripening washed-rind cheeses with whole-genome sequencing of community isolates. Sequencing-based approaches revealed a highly reproducible microbial succession in each cheese and the coexistence of closely related Psychrobacter species and enabled the prediction of plasmid and phage diversity and their host associations. In combination with culture-based approaches, we established a genomic catalog and a paired 16-member in vitro washed-rind cheese system. The combination of multi-platform metagenomic time-series data and an in vitro model provides a rich resource for further investigation of cheese rind microbiomes both computationally and experimentally. IMPORTANCE Metagenome sequencing can provide great insights into microbiome composition and function and help researchers develop testable hypotheses. Model microbiomes, such as those composed of cheese rind bacteria and fungi, allow the testing of these hypotheses in a controlled manner. Here, we first generated an extensive longitudinal metagenomic data set. This data set reveals successional dynamics, yields a phyla-spanning bacterial genomic catalog, associates mobile genetic elements with their hosts, and provides insights into functional enrichment of Psychrobacter in the cheese environment. Next, we show that members of the washed-rind cheese microbiome lend themselves to in vitro community reconstruction. This paired metagenomic data and in vitro system can thus be used as a platform for generating and testing hypotheses related to the dynamics within, and the functions associated with, cheese rind microbiomes.
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13
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Reuben RC, Langer D, Eisenhauer N, Jurburg SD. Universal drivers of cheese microbiomes. iScience 2023; 26:105744. [PMID: 36582819 PMCID: PMC9792889 DOI: 10.1016/j.isci.2022.105744] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/25/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022] Open
Abstract
The culinary value, quality, and safety of cheese are largely driven by the resident bacteria, but comparative analyses of the cheese microbiota across cheese types are scarce. We present the first global synthesis of cheese microbiomes. Following a systematic literature review of cheese microbiology research, we collected 16S rRNA gene amplicon sequence data from 824 cheese samples spanning 58 cheese types and 16 countries. We found a consistent, positive relationship between microbiome richness and pH, and a higher microbial richness in cheeses derived from goat milk. In contrast, we found no relationship between pasteurization, geographic location, or salinity and richness. Milk and cheese type, geographic location, and pasteurization collectively explained 65% of the variation in microbial community composition. Importantly, we identified four universal cheese microbiome types, driven by distinct dominant taxa. Our study reveals notable diversity patterns among the cheese microbiota, which are driven by geography and local environmental variables.
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Affiliation(s)
- Rine Christopher Reuben
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstraße 4, 04103 Leipzig, Germany
| | - Désirée Langer
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Nico Eisenhauer
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstraße 4, 04103 Leipzig, Germany
| | - Stephanie D. Jurburg
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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14
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Wang D, Meng Y, Meng F. Genome-centric metagenomics insights into functional divergence and horizontal gene transfer of denitrifying bacteria in anammox consortia. WATER RESEARCH 2022; 224:119062. [PMID: 36116192 DOI: 10.1016/j.watres.2022.119062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/21/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
Denitrifying bacteria with high abundances in anammox communities play crucial roles in achieving stable anammox-based systems. Despite the relative constant composition of denitrifying bacteria, their functional diversity remains to be explored in anammox communities. Herein, a total of 77 high-quality metagenome-assembled genomes (MAGs) of denitrifying bacteria were recovered from the anammox community in a full-scale swine wastewater treatment plant. Among these microbes, a total of 26 MAGs were affiliated with the seven dominant denitrifying genera that have total abundances higher than 1%. A meta-analysis of these species suggested that external organics reduced the abundances of genus Ignavibacterium and species MAG.305 of UTPRO2 in anammox communities. Comparative genome analysis revealed functional divergence across different denitrifying bacteria, largely owing to their distinct capabilities for carbohydrate (including endogenous and exogenous) utilization and vitamin (e.g., pantothenate and thiamine) biosynthesis. Serval microbes in this system contained fewer genes encoding biotin, pantothenate and methionine biosynthesis compared with their related species from other habitats. In addition, the genes encoding energy production and conversion (73 genes) and inorganic ion transport (53 genes) putatively transferred from other species to denitrifying bacteria, while these denitrifying bacteria (especially genera UTPRO2 and SCN-69-89) likely donated the genes encoding nutrients (e.g., inorganic ion and amino acid) transporter (64 genes) for other members to utilize new metabolites. Collectively, these findings highlighted the functional divergence of these denitrifying bacteria and speculated that the genetic interactions within anammox communities through horizontal gene transfer may be one of the reasons for their functional divergence.
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Affiliation(s)
- Depeng Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China
| | - Yabing Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China.
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15
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Garza DR, von Meijenfeldt FAB, van Dijk B, Boleij A, Huynen MA, Dutilh BE. Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes. BMC Ecol Evol 2022; 22:101. [PMID: 35974327 PMCID: PMC9382767 DOI: 10.1186/s12862-022-02052-3] [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: 09/13/2021] [Accepted: 07/22/2022] [Indexed: 11/15/2022] Open
Abstract
Background Microbial pan-genomes are shaped by a complex combination of stochastic and deterministic forces. Even closely related genomes exhibit extensive variation in their gene content. Understanding what drives this variation requires exploring the interactions of gene products with each other and with the organism’s external environment. However, to date, conceptual models of pan-genome dynamics often represent genes as independent units and provide limited information about their mechanistic interactions. Results We simulated the stochastic process of gene-loss using the pooled genome-scale metabolic reaction networks of 46 taxonomically diverse bacterial and archaeal families as proxies for their pan-genomes. The frequency by which reactions are retained in functional networks when stochastic gene loss is simulated in diverse environments allowed us to disentangle the metabolic reactions whose presence depends on the metabolite composition of the external environment (constrained by “nutrition”) from those that are independent of the environment (constrained by “nature”). By comparing the frequency of reactions from the first group with their observed frequencies in bacterial and archaeal families, we predicted the metabolic niches that shaped the genomic composition of these lineages. Moreover, we found that the lineages that were shaped by a more diverse metabolic niche also occur in more diverse biomes as assessed by global environmental sequencing datasets. Conclusion We introduce a computational framework for analyzing and interpreting pan-reactomes that provides novel insights into the ecological and evolutionary drivers of pan-genome dynamics. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02052-3.
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16
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Tong Z, Liu F, Tian Y, Zhang J, Liu H, Duan J, Bi W, Qin J, Xu S. Effect of biochar on antibiotics and antibiotic resistance genes variations during co-composting of pig manure and corn straw. Front Bioeng Biotechnol 2022; 10:960476. [PMID: 35979171 PMCID: PMC9377313 DOI: 10.3389/fbioe.2022.960476] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/30/2022] [Indexed: 12/03/2022] Open
Abstract
Pig manure is a reservoir of antibiotics and antibiotic resistance genes (ARGs). The effect of biochar on the variations in physicochemical properties, bacterial communities, antibiotics, ARGs, and mobile genetic elements (MGEs) of compost product during co-composting of pig manure and corn straw have been investigated in this study. Compared with the control treatment (CK), biochar addition accelerated the increase in pile temperature and prolonged the high temperature period (>55°C) for 2 days. Under biochar influence, organic matter degradation, NH4+-N conversion and NO3−-N production was accelerated, and dissolved total organic carbon (DOC) and dissolved total nitrogen (DTN) utilization by microorganisms were enhanced. Biochar addition altered the microbial community and promoted the vital activity of Actinobacteria in the later composting stage. The antibiotics removal efficiency (except danofloxacin and enrofloxacin) was accelerated in the early composting stage (1–14 days) by biochar addition, the pile temperature had a positive effect on antibiotics removal, and the total antibiotics removal efficiency in CK and CK+Biochar treatments was 69.58% and 78.67% at the end of the composting process, respectively. The absolute abundance of most of the ARGs in the CK+Biochar treatment was lower than that in the CK treatment during composting, and the ARGs removal mainly occurred in the early (1–14 days) and later (28–50 days) stages. Biochar addition reduced the absolute abundance of MGEs (intI1, intI2) in the compost product, and most of the ARGs had a significant positive correlation with MGEs. Network analysis and redundancy analysis showed that ARGs and MGEs occurred in various host bacteria (Firmicutes, Actinobacteria, Bacteroidetes, Proteobacteria, and Halanaerobiaeota), and that DTN and NH4+-N are the main factors regulating the changes in bacterial communities, antibiotics, ARGs, and MGEs during composting. Moreover, MGEs contributed the most to the variation in ARGs. In summary, biochar addition during composting accelerated antibiotics removal and inhibited accumulation and transmission of ARGs. The results of this study could provide theoretical and technical support for biochar application for antibiotics and ARGs removal during livestock and poultry manure composting.
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Affiliation(s)
- Zhenye Tong
- College of Resources and Environment, Shanxi Agricultural University, Jinzhong, China
| | - Fenwu Liu
- College of Resources and Environment, Shanxi Agricultural University, Jinzhong, China
- *Correspondence: Fenwu Liu,
| | - Yu Tian
- College of Resources and Environment, Shanxi Agricultural University, Jinzhong, China
| | - Jingzhi Zhang
- College of Resources and Environment, Shanxi Agricultural University, Jinzhong, China
| | - Hui Liu
- College of Resources and Environment, Shanxi Agricultural University, Jinzhong, China
| | - Jiaze Duan
- Nongshengyuan Family Farm, Jinzhong, China
| | - Wenlong Bi
- College of Resources and Environment, Shanxi Agricultural University, Jinzhong, China
| | - Junmei Qin
- College of Resources and Environment, Shanxi Agricultural University, Jinzhong, China
| | - Shaozu Xu
- College of Resources and Environment, Shanxi Agricultural University, Jinzhong, China
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17
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Yao S, Hao L, Zhou R, Jin Y, Huang J, Wu C. Multispecies biofilms in fermentation: Biofilm formation, microbial interactions, and communication. Compr Rev Food Sci Food Saf 2022; 21:3346-3375. [PMID: 35762651 DOI: 10.1111/1541-4337.12991] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 05/07/2022] [Accepted: 05/15/2022] [Indexed: 02/05/2023]
Abstract
Food fermentation is driven by microorganisms, which usually coexist as multispecies biofilms. The activities and interactions of functional microorganisms and pathogenic bacteria in biofilms have important implications for the quality and safety of fermented foods. It was verified that the biofilm lifestyle benefited the fitness of microorganisms in harsh environments and intensified the cooperation and competition between biofilm members. This review focuses on multispecies biofilm formation, microbial interactions and communication in biofilms, and the application of multispecies biofilms in food fermentation. Microbial aggregation and adhesion are important steps in the early stage of multispecies biofilm formation. Different biofilm-forming abilities and strategies among microorganisms lead to several types of multispecies biofilm formation. The spatial distribution of multispecies biofilms reflects microbial interactions and biofilm function. Then, we discuss the intrinsic factors and external manifestations of multispecies biofilm system succession. Several typical interspecies cooperation and competition modes and mechanisms of microbial communication were reviewed in this review. The main limitations of the studies included in this review are the relatively small number of studies of biofilms formed by functional microorganisms during fermentation and the lack of direct evidence for the formation process of multispecies biofilms and microbial interactions and communication within biofilms. This review aims to provide the food industry with a sufficient understanding of multispecies biofilms in food fermentation. Practical Application: Meanwhile, it offers a reference value for better controlling and utilizing biofilms during food fermentation process, and the improvement of the yield, quality, and safety of fermented products including Chinese Baijiu, cheeese,kefir, soy sauce, kombucha, and fermented olive.
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Affiliation(s)
- Shangjie Yao
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China.,Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Liying Hao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Rongqing Zhou
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China.,Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Yao Jin
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China.,Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Jun Huang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China.,Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Chongde Wu
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China.,Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
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18
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Kiousi DE, Efstathiou C, Tegopoulos K, Mantzourani I, Alexopoulos A, Plessas S, Kolovos P, Koffa M, Galanis A. Genomic Insight Into Lacticaseibacillus paracasei SP5, Reveals Genes and Gene Clusters of Probiotic Interest and Biotechnological Potential. Front Microbiol 2022; 13:922689. [PMID: 35783439 PMCID: PMC9244547 DOI: 10.3389/fmicb.2022.922689] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/16/2022] [Indexed: 12/22/2022] Open
Abstract
The Lacticaseibacillus paracasei species is comprised by nomadic bacteria inhabiting a wide variety of ecological niches, from fermented foodstuffs to host-associated microenvironments. Lc. paracasei SP5 is a novel strain, originally isolated from kefir grains that presents desirable probiotic and biotechnological attributes. In this study, we applied genomic tools to further characterize the probiotic and biotechnological potential of the strain. Firstly, whole genome sequencing and assembly, were performed to construct the chromosome map of the strain and determine its genomic stability. Lc. paracasei SP5 carriers several insertion sequences, however, no plasmids or mobile elements were detected. Furthermore, phylogenomic and comparative genomic analyses were utilized to study the nomadic attributes of the strain, and more specifically, its metabolic capacity and ability to withstand environmental stresses imposed during food processing and passage through the gastrointestinal (GI) tract. More specifically, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Carbohydrate-active enzyme (CAZymes) analyses provided evidence for the ability of the stain to utilize an array of carbohydrates as growth substrates. Consequently, genes for heat, cold, osmotic shock, acidic pH, and bile salt tolerance were annotated. Importantly bioinformatic analysis showed that the novel strain does not harbor acquired antimicrobial resistance genes nor virulence factors, in agreement with previous experimental data. Putative bacteriocin biosynthesis clusters were identified using BAGEL4, suggesting its potential antimicrobial activity. Concerning microbe-host interactions, adhesins, moonlighting proteins, exopolysaccharide (EPS) biosynthesis genes and pilins mediating the adhesive phenotype were, also, pinpointed in the genome of Lc. paracasei SP5. Validation of this phenotype was performed by employing a microbiological method and confocal microscopy. Conclusively, Lc. paracasei SP5 harbors genes necessary for the manifestation of the probiotic character and application in the food industry. Upcoming studies will focus on the mechanisms of action of the novel strain at multiple levels.
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Affiliation(s)
- Despoina Eugenia Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Christos Efstathiou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Konstantinos Tegopoulos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioanna Mantzourani
- Department of Agricultural Development, Democritus University of Thrace, Orestiada, Greece
| | - Athanasios Alexopoulos
- Department of Agricultural Development, Democritus University of Thrace, Orestiada, Greece
| | - Stavros Plessas
- Department of Agricultural Development, Democritus University of Thrace, Orestiada, Greece
- *Correspondence: Stavros Plessas,
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Maria Koffa
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
- Alex Galanis,
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19
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Wang R, Wu J, Jiang N, Lin H, An F, Wu C, Yue X, Shi H, Wu R. Recent developments in horizontal gene transfer with the adaptive innovation of fermented foods. Crit Rev Food Sci Nutr 2022; 63:569-584. [PMID: 35647734 DOI: 10.1080/10408398.2022.2081127] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Horizontal gene transfer (HGT) has contributed significantly to the adaptability of bacteria, yeast and mold in fermented foods, whose evidence has been found in several fermented foods. Although not every HGT has biological significance, it plays an important role in improving the quality of fermented foods. In this review, how HGT facilitated microbial domestication and adaptive evolution in fermented foods was discussed. HGT can assist in the industrial innovation of fermented foods, and this adaptive evolution strategy can improve the quality of fermented foods. Additionally, the mechanism underlying HGT in fermented foods were analyzed. Furthermore, the critical bottlenecks involved in optimizing HGT during the production of fermented foods and strategies for optimizing HGT were proposed. Finally, the prospect of HGT for promoting the industrial innovation of fermented foods was highlighted. The comprehensive report on HGT in fermented foods provides a new trend for domesticating preferable starters for food fermentation, thus optimizing the quality and improving the industrial production of fermented foods.
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Affiliation(s)
- Ruhong Wang
- College of Food Science, Shenyang Agricultural University, Shenyang, P.R. China
| | - Junrui Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, P.R. China.,Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang Agricultural University, Shenyang, P.R. China.,Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang Agricultural University, Shenyang, P.R. China
| | - Nan Jiang
- College of Food Science, Shenyang Agricultural University, Shenyang, P.R. China
| | - Hao Lin
- College of Food Science, Shenyang Agricultural University, Shenyang, P.R. China
| | - Feiyu An
- College of Food Science, Shenyang Agricultural University, Shenyang, P.R. China
| | - Chen Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, P.R. China
| | - Xiqing Yue
- College of Food Science, Shenyang Agricultural University, Shenyang, P.R. China.,Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang Agricultural University, Shenyang, P.R. China.,Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang Agricultural University, Shenyang, P.R. China
| | - Haisu Shi
- College of Food Science, Shenyang Agricultural University, Shenyang, P.R. China.,Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang Agricultural University, Shenyang, P.R. China.,Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang Agricultural University, Shenyang, P.R. China
| | - Rina Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, P.R. China.,Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang Agricultural University, Shenyang, P.R. China.,Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang Agricultural University, Shenyang, P.R. China
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20
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Comparative Genomics Unveils the Habitat Adaptation and Metabolic Profiles of
Clostridium
in an Artificial Ecosystem for Liquor Production. mSystems 2022; 7:e0029722. [PMID: 35491831 PMCID: PMC9238394 DOI: 10.1128/msystems.00297-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pit mud is a typical artificial ecosystem for Chinese liquor production.
Clostridium
inhabiting pit mud plays essential roles in the flavor formation of strong-flavor baijiu. The relative abundance of
Clostridium
increased with pit mud quality, further influencing the quality of baijiu.
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21
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A review of methods for the inference and experimental confirmation of microbial association networks in cheese. Int J Food Microbiol 2022; 368:109618. [DOI: 10.1016/j.ijfoodmicro.2022.109618] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/21/2022] [Accepted: 03/06/2022] [Indexed: 12/15/2022]
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22
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Rodríguez J, González-Guerra A, Vázquez L, Fernández-López R, Flórez AB, de la Cruz F, Mayo B. Isolation and phenotypic and genomic characterization of Tetragenococcus spp. from two Spanish traditional blue-veined cheeses made of raw milk. Int J Food Microbiol 2022; 371:109670. [DOI: 10.1016/j.ijfoodmicro.2022.109670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/28/2022] [Accepted: 04/02/2022] [Indexed: 11/27/2022]
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23
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24
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Aron AT, Petras D, Schmid R, Gauglitz JM, Büttel I, Antelo L, Zhi H, Nuccio SP, Saak CC, Malarney KP, Thines E, Dutton RJ, Aluwihare LI, Raffatellu M, Dorrestein PC. Native mass spectrometry-based metabolomics identifies metal-binding compounds. Nat Chem 2022; 14:100-109. [PMID: 34795435 PMCID: PMC8959065 DOI: 10.1038/s41557-021-00803-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 08/27/2021] [Indexed: 11/09/2022]
Abstract
Although metals are essential for the molecular machineries of life, systematic methods for discovering metal-small molecule complexes from biological samples are limited. Here, we describe a two-step native electrospray ionization-mass spectrometry method, in which post-column pH adjustment and metal infusion are combined with ion identity molecular networking, a rule-based data analysis workflow. This method enabled the identification of metal-binding compounds in complex samples based on defined mass (m/z) offsets of ion species with the same chromatographic profiles. As this native electrospray metabolomics approach is suited to the use of any liquid chromatography-mass spectrometry system to explore the binding of any metal, this method has the potential to become an essential strategy for elucidating metal-binding molecules in biology.
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Affiliation(s)
- Allegra T. Aron
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA,Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA,Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, USA,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA,Present affiliation: CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Tübingen, Tübingen, 72076, Germany
| | - Robin Schmid
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA,Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, D-48149, Germany
| | - Julia M. Gauglitz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA,Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093, USA,Present affiliation: Sapient Bioanalytics, La Jolla, CA, 92093, USA
| | - Isabell Büttel
- Institute of Molecular Physiology, Microbiology and Wine Research, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, Mainz D-55128, Germany
| | - Luis Antelo
- Institute of Biotechnology and Drug Research (IBWF gGmbH), Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, Mainz D-55128, Germany
| | - Hui Zhi
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Sean-Paul Nuccio
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Christina C. Saak
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kien P. Malarney
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eckhard Thines
- Institute of Molecular Physiology, Microbiology and Wine Research, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, Mainz D-55128, Germany,Institute of Biotechnology and Drug Research (IBWF gGmbH), Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, Mainz D-55128, Germany
| | - Rachel J. Dutton
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA,Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lihini I. Aluwihare
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Manuela Raffatellu
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA,Chiba University-University of California San Diego Center for Mucosal Immunology, Allergy, and Vaccines (CU-UCSD cMAV), La Jolla, CA 92093, United States of America,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA,Correspondence to
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25
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Geng N, Sun G, Liu WJ, Gao BC, Sun C, Xu C, Hua E, Xu L. Distribution, Phylogeny and Evolution of Clinical and Environmental Vibrio vulnificus Antibiotic-Resistant Genes. Evol Bioinform Online 2022; 18:11769343221134400. [PMID: 36404992 PMCID: PMC9669696 DOI: 10.1177/11769343221134400] [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: 04/11/2022] [Accepted: 09/22/2022] [Indexed: 11/17/2022] Open
Abstract
Vibrio vulnificus is an emergent marine pathogen and is the
cause of a deadly septicemia. However, the evolution mechanism of
antibiotic-resistant genes (ARGs) is still unclear. Twenty-two high-quality
complete genomes of V. vulnificus were obtained and grouped
into 16 clinical isolates and 6 environmental isolates. Genomic annotations
found 23 ARG orthologous genes, among which 14 ARGs were shared by V.
vulnificus and other Vibrio members. Furthermore,
those ARGs were located in their chromosomes, rather than in the plasmids.
Phylogenomic reconstruction based on single-copy orthologous protein sequences
and ARG protein sequences revealed that clinical and environmental V.
vulnificus isolates were in a scattered distribution. The
calculation of non-synonymous and synonymous substitutions indicated that most
of ARGs evolved under purifying selection with the
Ka/Ks ratios lower than one, while
h-ns, rsmA, and soxR in several clinical
isolates evolved under the positive selection with
Ka/Ks ratios >1. Our result indicated
that V. vulnificus antibiotic-resistant armory was not only
confined to clinical isolates, but to environmental ones as well and clinical
isolates inclined to accumulate beneficial non-synonymous substitutions that
could be retained to improve competitiveness.
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Affiliation(s)
- Nan Geng
- Key Laboratory for Technology in Rural Water Management of Zhejiang Province, Zhejiang University of Water Resources and Electric Power, Hangzhou, People’s Republic of China
| | - Guojin Sun
- Key Laboratory for Technology in Rural Water Management of Zhejiang Province, Zhejiang University of Water Resources and Electric Power, Hangzhou, People’s Republic of China
| | - Wen-Jia Liu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, People’s Republic of China
| | - Bin-Cheng Gao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, People’s Republic of China
| | - Cong Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, People’s Republic of China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd, Shaoxing, People’s Republic of China
| | - Cundong Xu
- Key Laboratory for Technology in Rural Water Management of Zhejiang Province, Zhejiang University of Water Resources and Electric Power, Hangzhou, People’s Republic of China
| | - Ertian Hua
- Key Laboratory for Technology in Rural Water Management of Zhejiang Province, Zhejiang University of Water Resources and Electric Power, Hangzhou, People’s Republic of China
| | - Lin Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, People’s Republic of China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd, Shaoxing, People’s Republic of China
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26
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Yang C, You L, Kwok LY, Jin H, Peng J, Zhao Z, Sun Z. Strain-level multiomics analysis reveals significant variation in cheeses from different regions. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.112043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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27
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Ferrocino I, Rantsiou K, Cocolin L. Investigating dairy microbiome: an opportunity to ensure quality, safety and typicity. Curr Opin Biotechnol 2021; 73:164-170. [PMID: 34474311 DOI: 10.1016/j.copbio.2021.08.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/01/2021] [Accepted: 08/06/2021] [Indexed: 11/19/2022]
Abstract
A detailed understanding of the microbiome of cheese and dairy products is key to the optimization of flavour, appearance, overall quality and safety. Microorganisms (including bacteria, yeasts, moulds and viruses, especially bacteriophages) from the environment can enter the dairy supply chain at multiple stages with several implications. The ability to track these microorganisms and to understand their function and interaction can be greatly enhanced by the use of high-throughput sequencing. Depending on the specific production technology, dairy products can harbor several strains and antibiotic-resistance genes that can potentially interact with the gut microbiome, once the product is ingested. Milk-associated or cheese-associated microbial communities with their interaction, function and diversity are a key factor for the dairy industry. Multi-omics approaches have been seldom utilized in literature and they need to be further considered. Studying the role, origin, diversity and function of the microbial species involved in the complex system of dairy production can help improve processes in several fields of application. Integrating an extensive sampling procedure with an extensive culture based methodology is necessary. To this end, local producers, and in general stakeholders, should be guided to discover and maintain their microbial diversity. A better management of microbial resources through precision fermentation processes will in turn reduce overall food losses and increase the possibility to use the microbiome in order to increase the local producers' income.
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Affiliation(s)
- Ilario Ferrocino
- DISAFA-Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
| | - Kalliopi Rantsiou
- DISAFA-Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
| | - Luca Cocolin
- DISAFA-Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy.
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28
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Tarracchini C, Milani C, Lugli GA, Mancabelli L, Fontana F, Alessandri G, Longhi G, Anzalone R, Viappiani A, Turroni F, van Sinderen D, Ventura M. Phylogenomic disentangling of the Bifidobacterium longum subsp. infantis taxon. Microb Genom 2021; 7. [PMID: 34319225 PMCID: PMC8477406 DOI: 10.1099/mgen.0.000609] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Members of the Bifidobacterium longum species have been shown to possess adaptive abilities to allow colonization of different mammalian hosts, including humans, primates and domesticated mammalian species, such as dogs, horses, cattle and pigs. To date, three subspecies have formally been recognized to belong to this bifidobacterial taxon, i.e. B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis. Although B. longum subsp. longum is widely distributed in the human gut irrespective of host age, B. longum subsp. infantis appears to play a significant role as a prominent member of the gut microbiota of breast-fed infants. Nevertheless, despite the considerable scientific relevance of these taxa and the vast body of genomic data now available, an accurate dissection of the genetic features that comprehensively characterize the B. longum species and its subspecies is still missing. In the current study, we employed 261 publicly available B. longum genome sequences, combined with those of 11 new isolates, to investigate genomic diversity of this taxon through comparative genomic and phylogenomic approaches. These analyses allowed us to highlight a remarkable intra-species genetic and physiological diversity. Notably, characterization of the genome content of members of B. longum subsp. infantis subspecies suggested that this taxon may have acquired genetic features for increased competitiveness in the gut environment of suckling hosts. Furthermore, specific B. longum subsp. infantis genomic features appear to be responsible for enhanced horizontal gene transfer (HGT) occurrences, underpinning an intriguing dedication toward acquisition of foreign DNA by HGT events.
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Affiliation(s)
- Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,GenProbio Srl, Parma, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,GenProbio Srl, Parma, Italy
| | | | | | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Ireland and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
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29
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Abstract
Bacteria acquire novel DNA through horizontal gene transfer (HGT), a process that enables an organism to rapidly adapt to changing environmental conditions, provides a competitive edge and potentially alters its relationship with its host. Although the HGT process is routinely exploited in laboratories, there is a surprising disconnect between what we know from laboratory experiments and what we know from natural environments, such as the human gut microbiome. Owing to a suite of newly available computational algorithms and experimental approaches, we have a broader understanding of the genes that are being transferred and are starting to understand the ecology of HGT in natural microbial communities. This Review focuses on these new technologies, the questions they can address and their limitations. As these methods are applied more broadly, we are beginning to recognize the full extent of HGT possible within a microbiome and the punctuated dynamics of HGT, specifically in response to external stimuli. Furthermore, we are better characterizing the complex selective pressures on mobile genetic elements and the mechanisms by which they interact with the bacterial host genome.
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Affiliation(s)
- Ilana Lauren Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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30
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Unraveling the world of halophilic and halotolerant bacteria in cheese by combining cultural, genomic and metagenomic approaches. Int J Food Microbiol 2021; 358:109312. [PMID: 34215422 DOI: 10.1016/j.ijfoodmicro.2021.109312] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 05/02/2021] [Accepted: 06/14/2021] [Indexed: 11/20/2022]
Abstract
Halophilic/halotolerant bacteria are generally assumed to live in natural environments, although they may also be found in foods such as cheese and seafood. These salt-loving bacteria have been occasionally characterized in cheese, and studies on their ecological and technological functions are still scarce. We therefore selected 13 traditional cheeses to systematically characterize these microorganisms in their rinds via cultural, genomic and metagenomic methods. Using different salt-based media, we identified 35 strains with unique 16S rRNA and rpoB gene sequences, whose whole genome was sequenced. Twenty are Gram-positive species including notably Brevibacterium aurantiacum (6) and Staphylococcus equorum (3), which are also frequently added as starters. ANI and pan-genomic analyses confirm the high genetic diversity of B. aurantiacum and reveal the presence of two subspecies in S. equorum, as well as the genetic proximity of several cheese strains to bovine isolates. Additionally, we isolated 15 Gram-negative strains, potentially defining ten new species of halophilic/halotolerant cheese bacteria, in particular for the genera Halomonas and Psychrobacter. The use of all the genomes sequenced in this study as a reference to complement those existing in the databases allowed us to study the representativeness of 66 species of halophilic/halotolerant bacteria in 74 cheese rind metagenomes. While Gram-positive strains may flourish in the different types of technologies, Gram-negative species are particularly abundant in cheeses with high moisture, such as washed-rind cheeses. Finally, analyses of co-occurrences reveal assemblies, including the frequent coexistence of several species of the same genus, forming moderately complex ecosystems with functional redundancies that probably ensure stable cheese development.
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31
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Sheinman M, Arkhipova K, Arndt PF, Dutilh BE, Hermsen R, Massip F. Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain. eLife 2021; 10:62719. [PMID: 34121661 PMCID: PMC8270642 DOI: 10.7554/elife.62719] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 06/13/2021] [Indexed: 12/19/2022] Open
Abstract
Horizontal gene transfer (HGT) is an essential force in microbial evolution. Despite detailed studies on a variety of systems, a global picture of HGT in the microbial world is still missing. Here, we exploit that HGT creates long identical DNA sequences in the genomes of distant species, which can be found efficiently using alignment-free methods. Our pairwise analysis of 93,481 bacterial genomes identified 138,273 HGT events. We developed a model to explain their statistical properties as well as estimate the transfer rate between pairs of taxa. This reveals that long-distance HGT is frequent: our results indicate that HGT between species from different phyla has occurred in at least 8% of the species. Finally, our results confirm that the function of sequences strongly impacts their transfer rate, which varies by more than three orders of magnitude between different functional categories. Overall, we provide a comprehensive view of HGT, illuminating a fundamental process driving bacterial evolution.
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Affiliation(s)
- Michael Sheinman
- Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands.,Division of Molecular Carcinogenesis, the Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ksenia Arkhipova
- Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands
| | - Peter F Arndt
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands
| | - Rutger Hermsen
- Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands
| | - Florian Massip
- Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany.,Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villleurbanne, France
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32
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Cosetta CM, Wolfe BE. Deconstructing and Reconstructing Cheese Rind Microbiomes for Experiments in Microbial Ecology and Evolution. ACTA ACUST UNITED AC 2021; 56:e95. [PMID: 31891451 DOI: 10.1002/cpmc.95] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cheese rind microbiomes are useful model systems for identifying the mechanisms that control microbiome diversity. Here, we describe the methods we have optimized to first deconstruct in situ cheese rind microbiome diversity and then reconstruct that diversity in laboratory environments to conduct controlled microbiome manipulations. Most cheese rind microbial species, including bacteria, yeasts, and filamentous fungi, can be easily cultured using standard lab media. Colony morphologies of taxa are diverse and can often be used to distinguish taxa at the phylum and sometimes even genus level. Through the use of cheese curd agar medium, thousands of unique community combinations or microbial interactions can be assessed. Transcriptomic experiments and transposon mutagenesis screens can pinpoint mechanisms of interactions between microbial species. Our general approach of creating a tractable synthetic microbial community from cheese can be easily applied to other fermented foods to develop other model microbiomes. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Isolation of cheese rind microbial communities Support Protocol 1: Preparation of plate count agar with milk and salt Basic Protocol 2: Identification of cheese rind bacterial and fungal isolates using 16S and ITS sequences Basic Protocol 3: Preparation of experimental glycerol stocks of yeasts and bacteria Basic Protocol 4: Preparation of experimental glycerol stocks of filamentous fungi Basic Protocol 5: Reconstruction of cheese rind microbial communities in vitro Support Protocol 2: Preparation of lyophilized and powdered cheese curd Support Protocol 3: Preparation of 10% cheese curd agar plates and tubes Basic Protocol 6: Interaction screens using responding lawns Support Protocol 4: Preparation of liquid 2% cheese curd Basic Protocol 7: Experimental evolution Basic Protocol 8: Measuring community function: pH/acidification Basic Protocol 9: Measuring community function: Pigment production Basic Protocol 10: RNA sequencing of cheese rind biofilms.
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Affiliation(s)
- Casey M Cosetta
- Department of Biology, Tufts University, Medford, Massachusetts
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33
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Distribution of ε-Poly-l-Lysine Synthetases in Coryneform Bacteria Isolated from Cheese and Human Skin. Appl Environ Microbiol 2021; 87:AEM.01841-20. [PMID: 33712427 PMCID: PMC8117764 DOI: 10.1128/aem.01841-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 03/07/2021] [Indexed: 12/23/2022] Open
Abstract
ε-Poly-l-lysine is a potent antimicrobial produced through fermentation of Streptomyces and used in many Asian countries as a food preservative. It is synthesized and excreted by a special nonribosomal peptide synthetase (NRPS)-like enzyme called Pls. In this study, we discovered a gene from cheese bacterium Corynebacterium variabile that showed high similarity to the Pls from Streptomyces in terms of domain architecture and gene context. By cloning it into Streptomyces coelicolor with a Streptomyces albulus Pls promoter, we confirmed that its product is indeed ε-poly-l-lysine. A comprehensive sequence analysis suggested that Pls genes are widely spread among coryneform actinobacteria isolated from cheese and human skin; 14 out of 15 Brevibacterium isolates and 10 out of 12 Corynebacterium isolates contain it in their genomes. This finding raises the possibility that ε-poly-l-lysine as a bioactive secondary metabolite might be produced and play a role in the cheese and skin ecosystems.IMPORTANCE Every year, microbial contamination causes billions of tons of food wasted and millions of cases of illness. ε-Poly-l-lysine has potent, wide-spectrum inhibitory activity and is heat stable and biodegradable. It has been approved for food preservation by an increasing number of countries. ε-Poly-l-lysine is produced from soil bacteria of the genus Streptomyces, also producers of various antibiotic drugs and toxins and not considered to be a naturally occurring food component. The frequent finding of pls in cheese and skin bacteria suggests that ε-poly-l-lysine may naturally exist in cheese and on our skin, and ε-poly-l-lysine producers are not limited to filamentous actinobacteria.
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34
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ODFM, an omics data resource from microorganisms associated with fermented foods. Sci Data 2021; 8:113. [PMID: 33879798 PMCID: PMC8058077 DOI: 10.1038/s41597-021-00895-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 03/23/2021] [Indexed: 11/08/2022] Open
Abstract
ODFM is a data management system that integrates comprehensive omics information for microorganisms associated with various fermented foods, additive ingredients, and seasonings (e.g. kimchi, Korean fermented vegetables, fermented seafood, solar salt, soybean paste, vinegar, beer, cheese, sake, and yogurt). The ODFM archives genome, metagenome, metataxonome, and (meta)transcriptome sequences of fermented food-associated bacteria, archaea, eukaryotic microorganisms, and viruses; 131 bacterial, 38 archaeal, and 28 eukaryotic genomes are now available to users. The ODFM provides both the Basic Local Alignment Search Tool search-based local alignment function as well as average nucleotide identity-based genetic relatedness measurement, enabling gene diversity and taxonomic analyses of an input query against the database. Genome sequences and annotation results of microorganisms are directly downloadable, and the microbial strains registered in the archive library will be available from our culture collection of fermented food-associated microorganisms. The ODFM is a comprehensive database that covers the genomes of an entire microbiome within a specific food ecosystem, providing basic information to evaluate microbial isolates as candidate fermentation starters for fermented food production.
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35
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Pierce EC, Morin M, Little JC, Liu RB, Tannous J, Keller NP, Pogliano K, Wolfe BE, Sanchez LM, Dutton RJ. Bacterial-fungal interactions revealed by genome-wide analysis of bacterial mutant fitness. Nat Microbiol 2021; 6:87-102. [PMID: 33139882 PMCID: PMC8515420 DOI: 10.1038/s41564-020-00800-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 09/16/2020] [Indexed: 11/09/2022]
Abstract
Microbial interactions are expected to be major determinants of microbiome structure and function. Although fungi are found in diverse microbiomes, their interactions with bacteria remain largely uncharacterized. In this work, we characterize interactions in 16 different bacterial-fungal pairs, examining the impacts of 8 different fungi isolated from cheese rind microbiomes on 2 bacteria (Escherichia coli and a cheese-isolated Pseudomonas psychrophila). Using random barcode transposon-site sequencing with an analysis pipeline that allows statistical comparisons between different conditions, we observed that fungal partners caused widespread changes in the fitness of bacterial mutants compared to growth alone. We found that all fungal species modulated the availability of iron and biotin to bacterial species, which suggests that these may be conserved drivers of bacterial-fungal interactions. Species-specific interactions were also uncovered, a subset of which suggested fungal antibiotic production. Changes in both conserved and species-specific interactions resulted from the deletion of a global regulator of fungal specialized metabolite production. This work highlights the potential for broad impacts of fungi on bacterial species within microbiomes.
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Affiliation(s)
- Emily C Pierce
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Manon Morin
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Jessica C Little
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Roland B Liu
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Joanna Tannous
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Food Research Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | | | - Laura M Sanchez
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Rachel J Dutton
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA, USA.
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36
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Li X, Cheng J, Liu X, Guo X, Liu Y, Fan W, Lu L, Ma Y, Liu T, Tao S, Jiang H. Origin and Evolution of Fusidane-Type Antibiotics Biosynthetic Pathway through Multiple Horizontal Gene Transfers. Genome Biol Evol 2020; 12:1830-1840. [PMID: 32915993 PMCID: PMC7750971 DOI: 10.1093/gbe/evaa163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2020] [Indexed: 01/08/2023] Open
Abstract
Fusidane-type antibiotics represented by fusidic acid, helvolic acid, and cephalosporin P1 have very similar core structures, but they are produced by fungi belonging to different taxonomic groups. The origin and evolution of fusidane-type antibiotics biosynthetic gene clusters (BGCs) in different antibiotics producing strains remained an enigma. In this study, we investigated the distribution and evolution of the fusidane BGCs in 1,284 fungal genomes. We identified 12 helvolic acid BGCs, 4 fusidic acid BGCs, and 1 cephalosporin P1 BGC in Pezizomycotina fungi. Phylogenetic analyses indicated six horizontal gene transfer (HGT) events in the evolutionary trajectory of the BGCs, including 1) three transfers across Eurotiomycetes and Sordariomycetes classes; 2) one transfer between genera under Sordariomycetes class; and 3) two transfers within Aspergillus genus under Eurotiomycetes classes. Finally, we proposed that the ancestor of fusidane BGCs would be originated from the Zoopagomycota by ancient HGT events according to the phylogenetic trees of key enzymes in fusidane BGCs (OSC and P450 genes). Our results extensively clarify the evolutionary trajectory of fusidane BGCs by HGT among distantly related fungi and provide new insights into the evolutionary mechanisms of metabolic pathways in fungi.
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Affiliation(s)
- Xiangchen Li
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Jian Cheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xiaonan Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xiaoxian Guo
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yuqian Liu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Wenjing Fan
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Lina Lu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yanhe Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Tao Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Shiheng Tao
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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37
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Saak CC, Dinh CB, Dutton RJ. Experimental approaches to tracking mobile genetic elements in microbial communities. FEMS Microbiol Rev 2020; 44:606-630. [PMID: 32672812 PMCID: PMC7476777 DOI: 10.1093/femsre/fuaa025] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022] Open
Abstract
Horizontal gene transfer is an important mechanism of microbial evolution and is often driven by the movement of mobile genetic elements between cells. Due to the fact that microbes live within communities, various mechanisms of horizontal gene transfer and types of mobile elements can co-occur. However, the ways in which horizontal gene transfer impacts and is impacted by communities containing diverse mobile elements has been challenging to address. Thus, the field would benefit from incorporating community-level information and novel approaches alongside existing methods. Emerging technologies for tracking mobile elements and assigning them to host organisms provide promise for understanding the web of potential DNA transfers in diverse microbial communities more comprehensively. Compared to existing experimental approaches, chromosome conformation capture and methylome analyses have the potential to simultaneously study various types of mobile elements and their associated hosts. We also briefly discuss how fermented food microbiomes, given their experimental tractability and moderate species complexity, make ideal models to which to apply the techniques discussed herein and how they can be used to address outstanding questions in the field of horizontal gene transfer in microbial communities.
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Affiliation(s)
- Christina C Saak
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Cong B Dinh
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Rachel J Dutton
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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38
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Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality. ACTA ACUST UNITED AC 2020; 1:500-510. [PMID: 37128079 DOI: 10.1038/s43016-020-0129-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 07/14/2020] [Indexed: 01/29/2023]
Abstract
A detailed understanding of the cheese microbiome is key to the optimization of flavour, appearance, quality and safety. Accordingly, we conducted a high-resolution meta-analysis of cheese microbiomes and corresponding volatilomes. Using 77 new samples from 55 artisanal cheeses from 27 Irish producers combined with 107 publicly available cheese metagenomes, we recovered 328 metagenome-assembled genomes, including 47 putative new species that could influence taste or colour through the secretion of volatiles or biosynthesis of pigments. Additionally, from a subset of samples, we found that differences in the abundances of strains corresponded with levels of volatiles. Genes encoding bacteriocins and other antimicrobials, such as pseudoalterin, were common, potentially contributing to the control of undesirable microorganisms. Although antibiotic-resistance genes were detected, evidence suggested they are not of major concern with respect to dissemination to other microbiomes. Phages, a potential cause of fermentation failure, were abundant and evidence for phage-mediated gene transfer was detected. The anti-phage defence mechanism CRISPR was widespread and analysis thereof, and of anti-CRISPR proteins, revealed a complex interaction between phages and bacteria. Overall, our results provide new and substantial technological and ecological insights into the cheese microbiome that can be applied to further improve cheese production.
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39
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A critical review of antibiotic resistance in probiotic bacteria. Food Res Int 2020; 136:109571. [PMID: 32846610 DOI: 10.1016/j.foodres.2020.109571] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/12/2022]
Abstract
Probiotics are defined as live microorganisms that, when administered in adequate amounts, confer a health benefit upon the host. At present, probiotics are gaining popularity worldwide and are widely used in food and medicine. Consumption of probiotics is increasing with further in-depth research on the relationship between intestinal flora and host health. Most people pay more attention to the function of probiotics but ignore their potential risks, such as infection and antibiotic resistance transfer to pathogenic microbes. Physiological functions, effects and mechanisms of action of probiotics were covered in this review, as well as the antibiotic resistance phenotypes, mechanisms and genes found in probiotics. Typical cases of antibiotic resistance of probiotics were also highlighted, as well as the potential risks (including pathogenicity, infectivity and excessive immune response) and corresponding strategies (dosage, formulation, and administration route). This timely study provides an avenue for further research, development and application of probiotics.
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40
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de Melo AG, Rousseau GM, Tremblay DM, Labrie SJ, Moineau S. DNA tandem repeats contribute to the genetic diversity of Brevibacterium aurantiacum phages. Environ Microbiol 2020; 22:3413-3428. [PMID: 32510858 DOI: 10.1111/1462-2920.15113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/23/2020] [Accepted: 06/02/2020] [Indexed: 12/16/2022]
Abstract
This report presents the characterization of the first virulent phages infecting Brevibacterium aurantiacum, a bacterial species used during the manufacture of surface-ripened cheeses. These phages were also responsible for flavour and colour defects in surface-ripened cheeses. Sixteen phages (out of 62 isolates) were selected for genome sequencing and comparative analyses. These cos-type phages with a long non-contractile tail currently belong to the Siphoviridae family (Caudovirales order). Their genome sizes vary from 35,637 to 36,825 bp and, similar to their host, have a high GC content (~61%). Genes encoding for an immunity repressor, an excisionase and a truncated integrase were found, suggesting that these virulent phages may be derived from a prophage. Their genomic organization is highly conserved, with most of the diversity coming from the presence of long (198 bp) DNA tandem repeats (TRs) within an open reading frame coding for a protein of unknown function. We categorized these phages into seven genomic groups according to their number of TR, which ranged from two to eight. Moreover, we showed that TRs are widespread in phage genomes, found in more than 85% of the genomes available in public databases.
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Affiliation(s)
- Alessandra G de Melo
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec City, Canada.,Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, Québec City, Canada
| | - Geneviève M Rousseau
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, Québec City, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de Médecine Dentaire, Université Laval, Québec, Québec City, Canada
| | - Denise M Tremblay
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, Québec City, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de Médecine Dentaire, Université Laval, Québec, Québec City, Canada
| | | | - Sylvain Moineau
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Québec City, Canada.,Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, Québec City, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de Médecine Dentaire, Université Laval, Québec, Québec City, Canada
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41
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Williams CL, Garcia-Reyero N, Martyniuk CJ, Tubbs CW, Bisesi JH. Regulation of endocrine systems by the microbiome: Perspectives from comparative animal models. Gen Comp Endocrinol 2020; 292:113437. [PMID: 32061639 DOI: 10.1016/j.ygcen.2020.113437] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/29/2020] [Accepted: 02/10/2020] [Indexed: 02/07/2023]
Abstract
The microbiome regulates endocrine systems and influences many aspects of hormone signaling. Using examples from different animal taxa, we highlight the state of the science in microbiome research as it relates to endocrinology and endocrine disruption research. Using a comparative approach discussing fish, birds, and mammals, we demonstrate the bidirectional interaction between microbiota and hormone systems, presenting concepts that include (1) gastrointestinal microbiome regulation of the neuroendocrine feeding axis; (2) stress hormones and microbial communities; (3) the role of site-specific microbiota in animal reproduction; (4) microbiome effects on the neuroendocrine systems and behavior; and (5) novel mechanisms of endocrine disruption through the microbiome. This mini-review demonstrates that hormones can directly affect the richness and diversity of microbiota and conversely, microbiota can influence hormone production and mediate their functions in animals. In addition, microbiota can influence the action of a diverse range of neurotransmitters and neuropeptides in the central nervous system, which can lead to behavioral disruptions. As many animals have species-specific reproductive behaviors, it is important to understand how shifts in the microbiota relate to these complex interactions between sexes. This is especially important for captive animals on specialized diets, and there are significant implications for microbiome research in conservation and reproductive biology. For example, microbial metabolites may modify motility of gametes or modulate hormone-receptor interactions in reproductive tissues. Thus, efforts to incorporate metabolomics into the science of microbiome-endocrine relationships, both those produced by the host and those generated from microbial metabolism, are increasingly needed. These concepts have fostered an exciting emerging era in comparative endocrinology.
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Affiliation(s)
- Candace L Williams
- Reproductive Sciences, San Diego Zoo Global Institute for Conservation Research, Escondido, CA 92027, USA.
| | - Natàlia Garcia-Reyero
- Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, MS 39180, USA
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Christopher W Tubbs
- Reproductive Sciences, San Diego Zoo Global Institute for Conservation Research, Escondido, CA 92027, USA
| | - Joseph H Bisesi
- Department of Environmental and Global Health and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA
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42
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Tanaka M, Kumakura D, Mino S, Doi H, Ogura Y, Hayashi T, Yumoto I, Cai M, Zhou YG, Gomez-Gil B, Araki T, Sawabe T. Genomic characterization of closely related species in the Rumoiensis clade infers ecogenomic signatures to non-marine environments. Environ Microbiol 2020; 22:3205-3217. [PMID: 32383332 DOI: 10.1111/1462-2920.15062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 04/21/2020] [Accepted: 05/03/2020] [Indexed: 11/28/2022]
Abstract
Members of the family Vibrionaceae are generally found in marine and brackish environments, playing important roles in nutrient cycling. The Rumoiensis clade is an unconventional group in the genus Vibrio, currently comprising six species from different origins including two species isolated from non-marine environments. In this study, we performed comparative genome analysis of all six species in the clade using their complete genome sequences. We found that two non-marine species, Vibrio casei and Vibrio gangliei, lacked the genes responsible for algal polysaccharide degradation, while a number of glycoside hydrolase genes were enriched in these two species. Expansion of insertion sequences was observed in V. casei and Vibrio rumoiensis, which suggests ongoing genomic changes associated with niche adaptations. The genes responsible for the metabolism of glucosylglycerate, a compound known to play a role as compatible solutes under nitrogen limitation, were conserved across the clade. These characteristics, along with genes encoding species-specific functions, may reflect the habit expansion which has led to the current distribution of Rumoiensis clade species. Genome analysis of all species in a single clade give us valuable insights into the genomic background of the Rumoiensis clade species and emphasize the genomic diversity and versatility of Vibrionaceae.
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Affiliation(s)
- Mami Tanaka
- Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Hakodate, Japan
| | - Daiki Kumakura
- Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Hakodate, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Hakodate, Japan
| | - Hidetaka Doi
- R&D Strategic Group, R&D Planning Department, Ajinomoto Co., Inc., Tokyo, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
| | - Man Cai
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bruno Gomez-Gil
- CIAD, AC Mazatlan Unit for Aquaculture and Environmental Management, Mazatlán, Sinaloa, AP 711, Mexico
| | - Toshiyoshi Araki
- Iga Community-based Research Institute, Mie University, Iga, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Hakodate, Japan
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43
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A Role for Gut Microbiome Fermentative Pathways in Fatty Liver Disease Progression. J Clin Med 2020; 9:jcm9051369. [PMID: 32392712 PMCID: PMC7291163 DOI: 10.3390/jcm9051369] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/24/2020] [Accepted: 05/03/2020] [Indexed: 02/06/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a multifactorial disease in which environmental and genetic factors are involved. Although the molecular mechanisms involved in NAFLD onset and progression are not completely understood, the gut microbiome (GM) is thought to play a key role in the process, influencing multiple physiological functions. GM alterations in diversity and composition directly impact disease states with an inflammatory course, such as non-alcoholic steatohepatitis (NASH). However, how the GM influences liver disease susceptibility is largely unknown. Similarly, the impact of strategies targeting the GM for the treatment of NASH remains to be evaluated. This review provides a broad insight into the role of gut microbiota in NASH pathogenesis, as a diagnostic tool, and as a therapeutic target in this liver disease. We highlight the idea that the balance in metabolic fermentations can be key in maintaining liver homeostasis. We propose that an overabundance of alcohol-fermentation pathways in the GM may outcompete healthier, acid-producing members of the microbiota. In this way, GM ecology may precipitate a self-sustaining vicious cycle, boosting liver disease progression.
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44
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Santos RG, Hurtado R, Gomes LGR, Profeta R, Rifici C, Attili AR, Spier SJ, Mazzullo G, Morais-Rodrigues F, Gomide ACP, Brenig B, Gala-García A, Cuteri V, Castro TLDP, Ghosh P, Seyffert N, Azevedo V. Complete genome analysis of Glutamicibacter creatinolyticus from mare abscess and comparative genomics provide insight of diversity and adaptation for Glutamicibacter. Gene 2020; 741:144566. [PMID: 32171826 DOI: 10.1016/j.gene.2020.144566] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/02/2019] [Accepted: 03/08/2020] [Indexed: 10/24/2022]
Abstract
Bacteria of the genusGlutamicibacterare considered ubiquitous because they can be found in soil, water and air. They have already been isolated from different habitats, including different types of soil, clinical samples, cheese and plants. Glutamicibacter creatinolyticus is a Gram-positive bacterium important to various biotechnological processes, however, as a pathogen it is associated to urinary tract infections and bacteremia. Recently,Glutamicibacter creatinolyticusLGCM 259 was isolated from a mare, which displayed several diffuse subcutaneous nodules with heavy vascularization. In this study, sequencing, genomic analysis ofG. creatinolyticusLGCM 259 and comparative analyseswere performedamong 4representatives of different members of genusfromdifferent habitats, available in the NCBI database. The LGCM 259 strain's genome carries important factors of bacterial virulence that are essential in cell viability, virulence, and pathogenicity. Genomic islands were predicted for 4 members of genusGlutamicibacter,showing ahigh number of GEIs,which may reflect a high interspecific diversity and a possible adaptive mechanism responsible for the survival of each species in its specific niche. Furthermore,G. creatinolyticusLGCM 259 sharessyntenicregions, albeit with a considerable loss of genes, in relation to the other species. In addition,G. creatinolyticusLGCM 259 presentsresistancegenes to 6 differentclasses ofantibiotics and heavy metals, such as: copper, arsenic, chromium and cobalt-zinc-cadmium.Comparative genomicsanalysescouldcontribute to the identification of mobile genetic elements particular to the speciesG. creatinolyticuscompared to other members of genus. The presence of specific regions inG. creatinolyticuscould be indicative of their rolesin host adaptation, virulence, and the characterization ofastrain that affects animals.
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Affiliation(s)
- Roselane Gonçalves Santos
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Raquel Hurtado
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Lucas Gabriel Rodrigues Gomes
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rodrigo Profeta
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Claudia Rifici
- Department of Veterinary Science, University of Messina (Italy), Polo Universitario, dell'Annunziata, 98168 Messina, ME, Italy
| | - Anna Rita Attili
- School of Biosciences and Veterinary Medicine, University of Camerino (Italy), Via Circonvallazione 93/95, 62024 Matelica, MC, Italy.
| | - Sharon J Spier
- Department of Veterinary Medicine and Epidemiology, University of California, Davis, CA, USA.
| | - Giuseppe Mazzullo
- Department of Veterinary Science, University of Messina (Italy), Polo Universitario, dell'Annunziata, 98168 Messina, ME, Italy.
| | - Francielly Morais-Rodrigues
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Anne Cybelle Pinto Gomide
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, Göttingen, Germany.
| | - Alfonso Gala-García
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil; Institute of Biological Sciences, Federal University of Para, PA, Brazil
| | - Vincenzo Cuteri
- School of Biosciences and Veterinary Medicine, University of Camerino (Italy), Via Circonvallazione 93/95, 62024 Matelica, MC, Italy.
| | - Thiago Luiz de Paula Castro
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil; Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Núbia Seyffert
- Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil
| | - Vasco Azevedo
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
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45
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Boto L, Pineda M, Pineda R. Potential impacts of horizontal gene transfer on human health and physiology and how anthropogenic activity can affect it. FEBS J 2019; 286:3959-3967. [PMID: 31495055 DOI: 10.1111/febs.15054] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/01/2019] [Accepted: 09/03/2019] [Indexed: 12/19/2022]
Abstract
Horizontal gene transfer (HGT) is widespread among prokaryotes driving their evolution. In this paper, we review the potential impact in humans of the HGT between prokaryotes living in close association with humans in two scenarios: horizontal transfer in human microbiomes and transfer between microbes living in human managed environments. Although our vision is focused on the possible impact of these transfers in the propagation of antibiotic resistance genes or pathogenicity determinants, we also discuss possible human physiological adaptations via gene transfer between resident and occasional bacteria in the human microbiome.
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Affiliation(s)
- Luis Boto
- Departamento DE Biodiversidad y Biologia Evolutiva, Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain
| | - Manuel Pineda
- Grupo Fisiologia Molecular y Biotecnologia de Plantas, Universidad dE Cordoba, Spain
| | - Rafael Pineda
- Instituto Maimonides de Investigacion Biomedica de Cordoba, Spain.,Departamento de Biologia Celular, Fisiologia e Inmunologia, Universidad de Cordoba, Spain
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46
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Reus E, Nielsen MR, Frandsen RJN. Metabolic and regulatory insights from the experimental horizontal gene transfer of the aurofusarin and bikaverin gene clusters to
Aspergillus nidulans. Mol Microbiol 2019; 112:1684-1700. [DOI: 10.1111/mmi.14376] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Elise Reus
- Department of Biotechnology and Bioengineering Technical University of Denmark Kongens Lyngby Denmark
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47
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May A, Narayanan S, Alcock J, Varsani A, Maley C, Aktipis A. Kombucha: a novel model system for cooperation and conflict in a complex multi-species microbial ecosystem. PeerJ 2019; 7:e7565. [PMID: 31534844 PMCID: PMC6730531 DOI: 10.7717/peerj.7565] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 07/29/2019] [Indexed: 01/02/2023] Open
Abstract
Kombucha, a fermented tea beverage with an acidic and effervescent taste, is composed of a multispecies microbial ecosystem with complex interactions that are characterized by both cooperation and conflict. In kombucha, a complex community of bacteria and yeast initiates the fermentation of a starter tea (usually black or green tea with sugar), producing a biofilm that covers the liquid over several weeks. This happens through several fermentative phases that are characterized by cooperation and competition among the microbes within the kombucha solution. Yeast produce invertase as a public good that enables both yeast and bacteria to metabolize sugars. Bacteria produce a surface biofilm which may act as a public good providing protection from invaders, storage for resources, and greater access to oxygen for microbes embedded within it. The ethanol and acid produced during the fermentative process (by yeast and bacteria, respectively) may also help to protect the system from invasion by microbial competitors from the environment. Thus, kombucha can serve as a model system for addressing important questions about the evolution of cooperation and conflict in diverse multispecies systems. Further, it has the potential to be artificially selected to specialize it for particular human uses, including the development of antimicrobial ecosystems and novel materials. Finally, kombucha is easily-propagated, non-toxic, and inexpensive, making it an excellent system for scientific inquiry and citizen science.
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Affiliation(s)
- Alexander May
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Psychology, Arizona State University, Tempe, AZ, USA
| | - Shrinath Narayanan
- The Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, AZ, USA
| | - Joe Alcock
- University of New Mexico, Albuquerque, NM, USA
| | - Arvind Varsani
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Carlo Maley
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- The Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, AZ, USA
| | - Athena Aktipis
- Department of Psychology, Arizona State University, Tempe, AZ, USA
- The Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, AZ, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
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48
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Pham NP, Landaud S, Lieben P, Bonnarme P, Monnet C. Transcription Profiling Reveals Cooperative Metabolic Interactions in a Microbial Cheese-Ripening Community Composed of Debaryomyces hansenii, Brevibacterium aurantiacum, and Hafnia alvei. Front Microbiol 2019; 10:1901. [PMID: 31474970 PMCID: PMC6706770 DOI: 10.3389/fmicb.2019.01901] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/02/2019] [Indexed: 11/13/2022] Open
Abstract
Ripening cultures containing fungi and bacteria are widely used in smear-ripened cheese production processes, but little is known about the biotic interactions of typical ripening microorganisms at the surface of cheese. We developed a lab-scale mini-cheese model to investigate the biotic interactions of a synthetic community that was composed of Debaryomyces hansenii, Brevibacterium aurantiacum, and Hafnia alvei, three species that are commonly used for smear-ripened cheese production. Transcriptomic analyses of cheese samples produced with different combinations of these three species revealed potential mechanisms of biotic interactions concerning iron acquisition, proteolysis, lipolysis, sulfur metabolism, and D-galactonate catabolism. A strong mutualistic interaction was observed between H. alvei and B. aurantiacum. We propose an explanation of this positive interaction in which B. aurantiacum would benefit from siderophore production by H. alvei, and the latter would be stimulated by the energy compounds liberated from caseins and triglycerides through the action of the proteases and lipases secreted by B. aurantiacum. In the future, it would be interesting to take the iron acquisition systems of cheese-associated strains into account for the purpose of improving the selection of the ripening culture components and their association in mixed cultures.
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Affiliation(s)
- Nguyen-Phuong Pham
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Sophie Landaud
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Pascale Lieben
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Pascal Bonnarme
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Christophe Monnet
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France
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49
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Somerville V, Lutz S, Schmid M, Frei D, Moser A, Irmler S, Frey JE, Ahrens CH. Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system. BMC Microbiol 2019; 19:143. [PMID: 31238873 PMCID: PMC6593500 DOI: 10.1186/s12866-019-1500-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/31/2019] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Complete and contiguous genome assemblies greatly improve the quality of subsequent systems-wide functional profiling studies and the ability to gain novel biological insights. While a de novo genome assembly of an isolated bacterial strain is in most cases straightforward, more informative data about co-existing bacteria as well as synergistic and antagonistic effects can be obtained from a direct analysis of microbial communities. However, the complexity of metagenomic samples represents a major challenge. While third generation sequencing technologies have been suggested to enable finished metagenome-assembled genomes, to our knowledge, the complete genome assembly of all dominant strains in a microbiome sample has not been demonstrated. Natural whey starter cultures (NWCs) are used in cheese production and represent low-complexity microbiomes. Previous studies of Swiss Gruyère and selected Italian hard cheeses, mostly based on amplicon metagenomics, concurred that three species generally pre-dominate: Streptococcus thermophilus, Lactobacillus helveticus and Lactobacillus delbrueckii. RESULTS Two NWCs from Swiss Gruyère producers were subjected to whole metagenome shotgun sequencing using the Pacific Biosciences Sequel and Illumina MiSeq platforms. In addition, longer Oxford Nanopore Technologies MinION reads had to be generated for one to resolve repeat regions. Thereby, we achieved the complete assembly of all dominant bacterial genomes from these low-complexity NWCs, which was corroborated by a 16S rRNA amplicon survey. Moreover, two distinct L. helveticus strains were successfully co-assembled from the same sample. Besides bacterial chromosomes, we could also assemble several bacterial plasmids and phages and a corresponding prophage. Biologically relevant insights were uncovered by linking the plasmids and phages to their respective host genomes using DNA methylation motifs on the plasmids and by matching prokaryotic CRISPR spacers with the corresponding protospacers on the phages. These results could only be achieved by employing long-read sequencing data able to span intragenomic as well as intergenomic repeats. CONCLUSIONS Here, we demonstrate the feasibility of complete de novo genome assembly of all dominant strains from low-complexity NWCs based on whole metagenomics shotgun sequencing data. This allowed to gain novel biological insights and is a fundamental basis for subsequent systems-wide omics analyses, functional profiling and phenotype to genotype analysis of specific microbial communities.
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Affiliation(s)
- Vincent Somerville
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
- SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Stefanie Lutz
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
- SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Michael Schmid
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
- SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Daniel Frei
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
| | - Aline Moser
- Agroscope, Research Group Biochemistry of Milk and Microorganisms, CH-3003 Bern, Switzerland
| | - Stefan Irmler
- Agroscope, Research Group Biochemistry of Milk and Microorganisms, CH-3003 Bern, Switzerland
| | - Jürg E. Frey
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
| | - Christian H. Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
- SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
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50
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Levesque S, de Melo AG, Labrie SJ, Moineau S. Mobilome of Brevibacterium aurantiacum Sheds Light on Its Genetic Diversity and Its Adaptation to Smear-Ripened Cheeses. Front Microbiol 2019; 10:1270. [PMID: 31244798 PMCID: PMC6579920 DOI: 10.3389/fmicb.2019.01270] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 05/22/2019] [Indexed: 11/13/2022] Open
Abstract
Brevibacterium aurantiacum is an actinobacterium that confers key organoleptic properties to washed-rind cheeses during the ripening process. Although this industrially relevant species has been gaining an increasing attention in the past years, its genome plasticity is still understudied due to the unavailability of complete genomic sequences. To add insights on the mobilome of this group, we sequenced the complete genomes of five dairy Brevibacterium strains and one non-dairy strain using PacBio RSII. We performed phylogenetic and pan-genome analyses, including comparisons with other publicly available Brevibacterium genomic sequences. Our phylogenetic analysis revealed that these five dairy strains, previously identified as Brevibacterium linens, belong instead to the B. aurantiacum species. A high number of transposases and integrases were observed in the Brevibacterium spp. strains. In addition, we identified 14 and 12 new insertion sequences (IS) in B. aurantiacum and B. linens genomes, respectively. Several stretches of homologous DNA sequences were also found between B. aurantiacum and other cheese rind actinobacteria, suggesting horizontal gene transfer (HGT). A HGT region from an iRon Uptake/Siderophore Transport Island (RUSTI) and an iron uptake composite transposon were found in five B. aurantiacum genomes. These findings suggest that low iron availability in milk is a driving force in the adaptation of this bacterial species to this niche. Moreover, the exchange of iron uptake systems suggests cooperative evolution between cheese rind actinobacteria. We also demonstrated that the integrative and conjugative element BreLI (Brevibacterium Lanthipeptide Island) can excise from B. aurantiacum SMQ-1417 chromosome. Our comparative genomic analysis suggests that mobile genetic elements played an important role into the adaptation of B. aurantiacum to cheese ecosystems.
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Affiliation(s)
- Sébastien Levesque
- Département de Biochimie, de microbiologie, et de Bio-informatique, Faculté des Sciences et de Génie, Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Quebec City, QC, Canada
| | - Alessandra G de Melo
- Département de Biochimie, de microbiologie, et de Bio-informatique, Faculté des Sciences et de Génie, Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Quebec City, QC, Canada
| | | | - Sylvain Moineau
- Département de Biochimie, de microbiologie, et de Bio-informatique, Faculté des Sciences et de Génie, Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Quebec City, QC, Canada.,Centre de Référence pour Virus Bactériens Félix d'Hérelle, Faculté de Médecine Dentaire, Université Laval, Quebec City, QC, Canada
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