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Rajguru B, Shri M, Bhatt VD. Exploring microbial diversity in the rhizosphere: a comprehensive review of metagenomic approaches and their applications. 3 Biotech 2024; 14:224. [PMID: 39247454 PMCID: PMC11379838 DOI: 10.1007/s13205-024-04065-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 08/26/2024] [Indexed: 09/10/2024] Open
Abstract
The rhizosphere, the soil region influenced by plant roots, represents a dynamic microenvironment where intricate interactions between plants and microorganisms shape soil health, nutrient cycling, and plant growth. Soil microorganisms are integral players in the transformation of materials, the dynamics of energy flows, and the intricate cycles of biogeochemistry. Considerable research has been dedicated to investigating the abundance, diversity, and intricacies of interactions among different microbes, as well as the relationships between plants and microbes present in the rhizosphere. Metagenomics, a powerful suite of techniques, has emerged as a transformative tool for dissecting the genetic repertoire of complex microbial communities inhabiting the rhizosphere. The review systematically navigates through various metagenomic approaches, ranging from shotgun metagenomics, enabling unbiased analysis of entire microbial genomes, to targeted sequencing of the 16S rRNA gene for taxonomic profiling. Each approach's strengths and limitations are critically evaluated, providing researchers with a nuanced understanding of their applicability in different research contexts. A central focus of the review lies in the practical applications of rhizosphere metagenomics in various fields including agriculture. By decoding the genomic content of rhizospheric microbes, researchers gain insights into their functional roles in nutrient acquisition, disease suppression, and overall plant health. The review also addresses the broader implications of metagenomic studies in advancing our understanding of microbial diversity and community dynamics in the rhizosphere. It serves as a comprehensive guide for researchers, agronomists, and policymakers, offering a roadmap for harnessing metagenomic approaches to unlock the full potential of the rhizosphere microbiome in promoting sustainable agriculture.
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Affiliation(s)
- Bhumi Rajguru
- School of Applied Sciences and Technology, Gujarat Technological University, Chandkheda, Ahmedabad, Gujarat India
| | - Manju Shri
- School of Applied Sciences and Technology, Gujarat Technological University, Chandkheda, Ahmedabad, Gujarat India
| | - Vaibhav D Bhatt
- School of Applied Sciences and Technology, Gujarat Technological University, Chandkheda, Ahmedabad, Gujarat India
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Parente E, Ricciardi A. A Comprehensive View of Food Microbiota: Introducing FoodMicrobionet v5. Foods 2024; 13:1689. [PMID: 38890917 PMCID: PMC11171936 DOI: 10.3390/foods13111689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
Amplicon-targeted metagenomics is now the standard approach for the study of the composition and dynamics of food microbial communities. Hundreds of papers on this subject have been published in scientific journals and the information is dispersed in a variety of sources, while raw sequences and their metadata are available in public repositories for some, but not all, of the published studies. A limited number of web resources and databases allow scientists to access this wealth of information but their level of annotation on studies and samples varies. Here, we report on the release of FoodMicrobionet v5, a comprehensive database of metataxonomic studies on bacterial and fungal communities of foods. The current version of the database includes 251 published studies (11 focusing on fungal microbiota, 230 on bacterial microbiota, and 10 providing data for both bacterial and fungal microbiota) and 14,035 samples with data on bacteria and 1114 samples with data on fungi. The new structure of the database is compatible with interactive apps and scripts developed for previous versions and allows scientists, R&D personnel in industries and regulators to access a wealth of information on food microbial communities.
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Affiliation(s)
- Eugenio Parente
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, 85100 Potenza, Italy;
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Iqbal S, Begum F, Ullah I, Jalal N, Shaw P. Peeling off the layers from microbial dark matter (MDM): recent advances, future challenges, and opportunities. Crit Rev Microbiol 2024:1-21. [PMID: 38385313 DOI: 10.1080/1040841x.2024.2319669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 02/10/2024] [Indexed: 02/23/2024]
Abstract
Microbes represent the most common organisms on Earth; however, less than 2% of microbial species in the environment can undergo cultivation for study under laboratory conditions, and the rest of the enigmatic, microbial world remains mysterious, constituting a kind of "microbial dark matter" (MDM). In the last two decades, remarkable progress has been made in culture-dependent and culture-independent techniques. More recently, studies of MDM have relied on culture-independent techniques to recover genetic material through either unicellular genomics or shotgun metagenomics to construct single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs), respectively, which provide information about evolution and metabolism. Despite the remarkable progress made in the past decades, the functional diversity of MDM still remains uncharacterized. This review comprehensively summarizes the recently developed culture-dependent and culture-independent techniques for characterizing MDM, discussing major challenges, opportunities, and potential applications. These activities contribute to expanding our knowledge of the microbial world and have implications for various fields including Biotechnology, Bioprospecting, Functional genomics, Medicine, Evolutionary and Planetary biology. Overall, this review aims to peel off the layers from MDM, shed light on recent advancements, identify future challenges, and illuminate the exciting opportunities that lie ahead in unraveling the secrets of this intriguing microbial realm.
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Affiliation(s)
- Sajid Iqbal
- Oujiang Lab (Zhejiang Laboratory for Regenerative Medicine, Vision, and Brain Health), Wenzhou, China
- School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, China
| | - Farida Begum
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Ihsan Ullah
- College of Chemical Engineering, Fuzhou University, Fuzhou, China
| | - Nasir Jalal
- Oujiang Lab (Zhejiang Laboratory for Regenerative Medicine, Vision, and Brain Health), Wenzhou, China
| | - Peter Shaw
- Oujiang Lab (Zhejiang Laboratory for Regenerative Medicine, Vision, and Brain Health), Wenzhou, China
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Zhang H, Zhang H, Du H, Yu X, Xu Y. The insights into the phage communities of fermented foods in the age of viral metagenomics. Crit Rev Food Sci Nutr 2024:1-13. [PMID: 38214674 DOI: 10.1080/10408398.2023.2299323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Phages play a critical role in the assembly and regulation of fermented food microbiome through lysis and lysogenic lifestyle, which in turn affects the yield and quality of fermented foods. Therefore, it is important to investigate and characterize the diversity and function of phages under complex microbial communities and nutrient substrate conditions to provide novel insights into the regulation of traditional spontaneous fermentation. Viral metagenomics has gradually garnered increasing attention in fermented food research to elucidate phage functions and characterize the interactions between phages and the microbial community. Advances in this technology have uncovered a wide range of phages associated with the production of traditional fermented foods and beverages. This paper reviews the common methods of viral metagenomics applied in fermented food research, and summarizes the ecological functions of phages in traditional fermented foods. In the future, combining viral metagenomics with culturable methods and metagenomics will broaden the scope of research on fermented food systems, revealing the complex role of phages and intricate phage-bacterium interactions.
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Affiliation(s)
- Huadong Zhang
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hongxia Zhang
- College of Life Sciences, Shanxi Normal University, Taiyuan, Shanxi, China
| | - Hai Du
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiaowei Yu
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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Cocconcelli PS, Gatti M, Giraffa G, Gobbetti M, Lanciotti R, Morelli L, Neviani E, Parente E. Should the microbiota of raw milk cheeses play a role in the definition of geographical indications and quality schemes within the European Union? mSystems 2023; 8:e0052023. [PMID: 37916828 PMCID: PMC10734520 DOI: 10.1128/msystems.00520-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Affiliation(s)
| | | | | | | | | | - Lorenzo Morelli
- Università Cattolica del Sacro Cuore, Piacenza-Cremona, Italy
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Walsh LH, Coakley M, Walsh AM, Crispie F, O’Toole PW, Cotter PD. Analysis of the milk kefir pan-metagenome reveals four community types, core species, and associated metabolic pathways. iScience 2023; 26:108004. [PMID: 37841598 PMCID: PMC10568436 DOI: 10.1016/j.isci.2023.108004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/14/2023] [Accepted: 09/18/2023] [Indexed: 10/17/2023] Open
Abstract
A comprehensive metagenomics-based investigation of the microorganisms present within milk kefir communities from across the globe was carried out with a view to defining the milk kefir pan-metagenome, including details relating to core and non-core components. Milk kefir samples, generated by inoculating full fat, pasteurized cow's milk with 64 kefir grains sourced from 25 different countries, were analyzed. We identified core features, including a consistent pattern of domination by representatives from the species Lactobacillus helveticus or the sub-species Lactobacillus kefiranofaciens subsp. kefiranofaciens, Lactococcus lactis subsp. lactis or Lla. cremoris subsp. cremoris in each kefir. Notably, even in kefirs where the lactococci did not dominate, they and 51 associated metabolic pathways were identified across all metagenomes. These insights can contribute to future efforts to create tailored kefir-based microbial communities for different applications and assist regulators and producers to ensure that kefir products have a microbial composition that reflects the artisanal beverage.
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Affiliation(s)
- Liam H. Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- School of Microbiology, University College Cork, Ireland
| | - Mairéad Coakley
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Aaron M. Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Paul W. O’Toole
- School of Microbiology, University College Cork, Ireland
- APC Microbiome Ireland SFI Research Centre, University College Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland SFI Research Centre, University College Cork, Ireland
- VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
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Nam NN, Do HDK, Loan Trinh KT, Lee NY. Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions. Foods 2023; 12:2140. [PMID: 37297385 PMCID: PMC10252221 DOI: 10.3390/foods12112140] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.
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Affiliation(s)
- Nguyen Nhat Nam
- Biotechnology Center, School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh City 87000, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ward 13, District 04, Ho Chi Minh City 72820, Vietnam
| | - Kieu The Loan Trinh
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea;
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea;
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Ammoun I, Kothe CI, Mohellibi N, Beal C, Yaacoub R, Renault P. Lebanese fermented goat milk products: From tradition to meta-omics. Food Res Int 2023; 168:112762. [PMID: 37120212 DOI: 10.1016/j.foodres.2023.112762] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023]
Abstract
Ambriss, Serdaleh and Labneh El Darff are traditional Lebanese products made from fermented goat's milk. A questionnaire completed by 50 producers of these products showed that they are prepared by periodic percolation either by milk or by Laban in amphora or goat skins during the lactation season. Production is carried out on a small scale and in a limited number of production units, often by elderly people, resulting in a real risk of disappearance of these products and loss of the corresponding microbial resources. In this study, 34 samples from 18 producers were characterized by culture-dependent and -independent analyses. The results obtained from these two methods were radically different, the latter revealing in Ambriss and Serdaleh the co-dominance of Lactobacillus kefiranofaciens, a fastidious-growing species, and Lactococcus lactis in a viable but not culturable state. Overall, their composition is reminiscent of kefir grains. Phylogenomic and functional analyses of the genomes of the key species Lb. kefiranofaciens have revealed differences from those found in kefir, particularly in their polysaccharide genes, which may explain the absence of grains. However, Labneh El Darff displayed a dominance of Lactobacillus delbrueckii, probably due to the addition of Laban. In addition, the study identified several zoonotic pathogens, including Streptococcus parasuis, which dominated in one sample. Metagenome-Assembled Genome (MAG) analysis indicated that this pathogen acquired lactose utilization genes through horizontal gene transfer. The contamination of the herd with Mycoplasmopsis agalactiae in the Chouf region was also revealed by MAG analysis of the Serdaleh samples. Antibiotic resistance genes were detected in most of the samples, particularly in the Serdaleh ones, where the dominant L. lactis strains possessed a plasmid with a multi-resistance island. Finally, this study paves the way for further analyses to shed light on the resilience of these ecosystems established in amphora or in goatskins and to improve hygiene practices for milk production.
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Affiliation(s)
- I Ammoun
- Université Paris-Saclay, INRAE, Micalis Institute, 78350 Jouy-en-Josas, France; Lebanese Agricultural Research Institute (LARI), Milk and Milk Products Department, Fanar, Lebanon
| | - C I Kothe
- Université Paris-Saclay, INRAE, Micalis Institute, 78350 Jouy-en-Josas, France; Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - N Mohellibi
- Université Paris-Saclay, INRAE, Micalis Institute, 78350 Jouy-en-Josas, France
| | - C Beal
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91120, Palaiseau, France
| | - R Yaacoub
- Lebanese University, Faculty of Agricultural and Veterinary Sciences, Food Science and Technology Department, Dekwaneh, Lebanon
| | - P Renault
- Université Paris-Saclay, INRAE, Micalis Institute, 78350 Jouy-en-Josas, France.
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