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Wanapat M, Dagaew G, Sommai S, Matra M, Suriyapha C, Prachumchai R, Muslykhah U, Phupaboon S. The application of omics technologies for understanding tropical plants-based bioactive compounds in ruminants: a review. J Anim Sci Biotechnol 2024; 15:58. [PMID: 38689368 PMCID: PMC11062008 DOI: 10.1186/s40104-024-01017-4] [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: 11/11/2023] [Accepted: 02/29/2024] [Indexed: 05/02/2024] Open
Abstract
Finding out how diet impacts health and metabolism while concentrating on the functional qualities and bioactive components of food is the crucial scientific objective of nutritional research. The complex relationship between metabolism and nutrition could be investigated with cutting-edge "omics" and bioinformatics techniques. This review paper provides an overview of the use of omics technologies in nutritional research, with a particular emphasis on the new applications of transcriptomics, proteomics, metabolomics, and genomes in functional and biological activity research on ruminant livestock and products in the tropical regions. A wealth of knowledge has been uncovered regarding the regulation and use of numerous physiological and pathological processes by gene, mRNA, protein, and metabolite expressions under various physiological situations and guidelines. In particular, the components of meat and milk were assessed using omics research utilizing the various methods of transcriptomics, proteomics, metabolomics, and genomes. The goal of this review is to use omics technologies-which have been steadily gaining popularity as technological tools-to develop new nutritional, genetic, and leadership strategies to improve animal products and their quality control. We also present an overview of the new applications of omics technologies in cattle production and employ nutriomics and foodomics technologies to investigate the microbes in the rumen ecology. Thus, the application of state-of-the-art omics technology may aid in our understanding of how species and/or breeds adapt, and the sustainability of tropical animal production, in the long run, is becoming increasingly important as a means of mitigating the consequences of climate change.
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Affiliation(s)
- Metha Wanapat
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Gamonmas Dagaew
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Sukruthai Sommai
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Maharach Matra
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Chaichana Suriyapha
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Rittikeard Prachumchai
- Department of Animal Science, Faculty of Agricultural Technology, University of Technology Thanyaburi, Rajamangala Pathum Thani, 12130, Thailand
| | - Uswatun Muslykhah
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Srisan Phupaboon
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand.
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Dixit S, Kumar S, Sharma R, Banakar PS, Singh M, Keshri A, Tyagi AK. Rumen multi-omics addressing diet-host-microbiome interplay in farm animals: a review. Anim Biotechnol 2023; 34:3187-3205. [PMID: 35713100 DOI: 10.1080/10495398.2022.2078979] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Continuous improvement in the living standards of developing countries, calls for an urgent need of high quality meat and dairy products. The farm animals have a micro-ecosystem in gastro-intestinal tract, comprising of a wide variety of flora and fauna which converts roughages and agricultural byproducts as well as nutrient rich concentrate sources into the useful products such as volatile fatty acids and microbial crude proteins. The microbial diversity changes according to composition of the feed, host species/breed and host's individual genetic makeup. From culture methods to next-generation sequencing technologies, the knowledge has emerged a lot to know-how of microbial world viz. their identification, enzymatic activities and metabolites which are the keys of ruminant's successful existence. The structural composition of ruminal community revealed through metagenomics can be elaborated by metatranscriptomics and metabolomics through deciphering their functional role in metabolism and their responses to the external and internal stimuli. These highly sophisticated analytical tools have made possible to correlate the differences in the feed efficiency, nutrients utilization and methane emissions to their rumen microbiome. The comprehensively understood rumen microbiome will enhance the knowledge in the fields of animal nutrition, biotechnology and climatology through deciphering the significance of each and every domain of residing microbial entity. The present review undertakes the recent investigations regarding rumen multi-omics viz. taxonomic and functional potential of microbial populations, host-diet-microbiome interactions and correlation with metabolic dynamics.
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Affiliation(s)
- Sonam Dixit
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Sachin Kumar
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Ritu Sharma
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - P S Banakar
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Manvendra Singh
- Krishi Vigyan Kendra, Banda University of Agriculture and Technology, Banda, India
| | - Anchal Keshri
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - A K Tyagi
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
- Animal Nutrition and Physiology, Indian Council of Agricultural Research, New Delhi, India
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Resendiz-Nava CN, Alonso-Onofre F, Silva-Rojas HV, Rebollar-Alviter A, Rivera-Pastrana DM, Stasiewicz MJ, Nava GM, Mercado-Silva EM. Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture System. Microorganisms 2023; 11:1633. [PMID: 37512805 PMCID: PMC10383152 DOI: 10.3390/microorganisms11071633] [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: 05/18/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Tomato is the main vegetable cultivated under soilless culture systems (SCSs); production of organic tomato under SCSs has increased due to consumer demands for healthier and environmentally friendly vegetables. However, organic tomato production under SCSs has been associated with low crop performance and fruit quality defects. These agricultural deficiencies could be linked to alterations in tomato plant microbiota; nonetheless, this issue has not been sufficiently addressed. Thus, the main goal of the present study was to characterize the rhizosphere and phyllosphere of tomato plants cultivated under conventional and organic SCSs. To accomplish this goal, tomato plants grown in commercial greenhouses under conventional or organic SCSs were tested at 8, 26, and 44 weeks after seedling transplantation. Substrate (n = 24), root (n = 24), and fruit (n = 24) composite samples were subjected to DNA extraction and high-throughput 16S rRNA gene sequencing. The present study revealed that the tomato core microbiota was predominantly constituted by Proteobacteria, Actinobacteria, and Firmicutes. Remarkably, six bacterial families, Bacillaceae, Microbacteriaceae, Nocardioidaceae, Pseudomonadaceae, Rhodobacteraceae, and Sphingomonadaceae, were shared among all substrate, rhizosphere, and fruit samples. Importantly, it was shown that plants under organic SCSs undergo a dysbiosis characterized by significant changes in the relative abundance of Bradyrhizobiaceae, Caulobacteraceae, Chitinophagaceae, Enterobacteriaceae, Erythrobacteraceae, Flavobacteriaceae, Nocardioidaceae, Rhodobacteraceae, and Streptomycetaceae. These results suggest that microbial alterations in substrates, roots, and fruits could be potential factors in contributing to the crop performance and fruit quality deficiencies observed in organic SCSs.
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Affiliation(s)
- Carolina N Resendiz-Nava
- Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, Mexico
| | | | - Hilda V Silva-Rojas
- Posgrado en Recursos Geneticos y Productividad, Produccion de Semillas, Colegio de Postgraduados, Km 36.5 Carretera Mexico-Texcoco, Texcoco 56264, Mexico
| | - Angel Rebollar-Alviter
- Centro Regional Morelia, Universidad Autonoma de Chapingo, Morelia 58170, Michoacan, Mexico
| | - Dulce M Rivera-Pastrana
- Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, Mexico
| | - Matthew J Stasiewicz
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, 1302W Pennsylvania Ave, Urbana, IL 61801, USA
| | - Gerardo M Nava
- Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, Mexico
| | - Edmundo M Mercado-Silva
- Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, Mexico
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You Y, Chi Y, Chen X, Wang J, Wang R, Li R, Chu S, Yang X, Zhang D, Zhou P. A sustainable approach for bioremediation of secondary salinized soils: Studying remediation efficiency and soil nitrate transformation by bioaugmentation. CHEMOSPHERE 2022; 300:134580. [PMID: 35421442 DOI: 10.1016/j.chemosphere.2022.134580] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/27/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
Nitrate is the main nitrogen source for plant growth, but it can also pollute the environment. A major cause of soil secondary salinization is the rising level of nitrates in the soil, which poses a threat to the sustainability and fertility of global greenhouse soils. Herein, Bacillus megaterium NCT-2 was used as a microbial agent to remove nitrate by bioaugmentation, and the remediation efficiency of secondary salinized soil in different degrees was evaluated. The findings showed that the highest nitrate removal rate of 62.76% was in a medium degree of secondary salinized soil. Moreover, the results of 16S rRNA high-throughput sequencing and quantitative real-time PCR (qPCR) demonstrated that NCT-2 agent reduced the microbial diversity, increased the microbial community stability, and changed the composition and function of the microbial community were changed by NCT-2 agent in all districts soil. Further analysis demonstrated that the NCT-2 bacterial agent significantly increased the key enzyme genes of the assimilation pathway (nitrite reductase gene NasD, 87-404 times, and glutamine reduction enzyme gene GlnA, 13-52 times) and dissimilatory reduction to ammonium (DNRA) (nitrate reductase gene NarG, 14-56 times) in different degrees of secondary salinized soils. This proved that NCT-2 agent could promote the nitrate assimilation and the dissimilation and reduction to ammonium in secondary salinized soil. Thus, the current findings suggested that the NCT-2 agent has a significant potential for reducing excessive nitrate levels in secondary salinized soil. The remediation efficiency was related to the microbial community composition and the degree of secondary salinization. This study could provide a theoretical basis for the remediation of secondary salinized soil in the future.
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Affiliation(s)
- Yimin You
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, China; Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, 800 Dongchuan Rd., Shanghai, 200240, China; Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Yaowei Chi
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, China; Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, 800 Dongchuan Rd., Shanghai, 200240, China; Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Xunfeng Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, China; Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, 800 Dongchuan Rd., Shanghai, 200240, China; Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Juncai Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, China; Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, 800 Dongchuan Rd., Shanghai, 200240, China; Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Renyuan Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, China; Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, 800 Dongchuan Rd., Shanghai, 200240, China; Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Ruotong Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, China
| | - Shaohua Chu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, China; Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, 800 Dongchuan Rd., Shanghai, 200240, China; Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Xijia Yang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, China; Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, 800 Dongchuan Rd., Shanghai, 200240, China; Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Dan Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, China; Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, 800 Dongchuan Rd., Shanghai, 200240, China; Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China.
| | - Pei Zhou
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, China; Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, 800 Dongchuan Rd., Shanghai, 200240, China; Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China.
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5
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Understanding microbial networks of farm animals through genomics, metagenomics and other meta-omic approaches for livestock wellness and sustainability. ANNALS OF ANIMAL SCIENCE 2022. [DOI: 10.2478/aoas-2022-0002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Abstract
The association of microorganisms with livestock as endosymbionts, opportunists, and pathogens has been a matter of debate for a long time. Several livestock-associated bacterial and other microbial species have been identified and characterized through traditional culture-dependent genomic approaches. However, it is imperative to understand the comprehensive microbial network of domestic animals for their wellness, disease management, and disease transmission control. Since it is strenuous to provide a niche replica to any microorganisms while culturing them, thus a substantial number of microbial communities remain obscure. Metagenomics has laid out a powerful lens for gaining insight into the hidden microbial diversity by allowing the direct sequencing of the DNA isolated from any livestock sample like the gastrointestinal tract, udder, or genital system. Through metatranscriptomics and metabolomics, understanding gene expression profiles of the microorganisms and their molecular phenotype has become unchallenging. With large data sets emerging out of the genomic, metagenomic, and other meta-omics methods, several computational tools have also been developed for curation, assembly, gene prediction, and taxonomic profiling of the microorganisms. This review provides a detailed account of the beneficial and pathogenic organisms that dwell within or on farm animals. Besides, it highlights the role of meta-omics and computational tools in a comprehensive analysis of livestock-associated microorganisms.
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Ribeiro DM, Salama AAK, Vitor ACM, Argüello A, Moncau CT, Santos EM, Caja G, de Oliveira JS, Balieiro JCC, Hernández-Castellano LE, Zachut M, Poleti MD, Castro N, Alves SP, Almeida AM. The application of omics in ruminant production: a review in the tropical and sub-tropical animal production context. J Proteomics 2020; 227:103905. [PMID: 32712373 DOI: 10.1016/j.jprot.2020.103905] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/25/2020] [Accepted: 07/16/2020] [Indexed: 02/08/2023]
Abstract
The demand for animal products (e.g. dairy and beef) in tropical regions is expected to increase in parallel with the public demand for sustainable practices, due to factors such as population growth and climate change. The necessity to increase animal production output must be achieved with better management and production technologies. For this to happen, novel research methodologies, animal selection and postgenomic tools play a pivotal role. Indeed, improving breeder selection programs, the quality of meat and dairy products as well as animal health will contribute to higher sustainability and productivity. This would surely benefit regions where resource quality and quantity are increasingly unstable, and research is still very incipient, which is the case of many regions in the tropics. The purpose of this review is to demonstrate how omics-based approaches play a major role in animal science, particularly concerning ruminant production systems and research associated to the tropics and developing countries. SIGNIFICANCE: Environmental conditions in the tropics make livestock production harder, compared to temperate regions. Due to global warming, the sustainability of livestock production will become increasingly problematic. The use of novel omics technologies could generate useful information to understand adaptation mechanisms of resilient breeds and/or species. The application of omics to tropical animal production is still residual in the currently available literature. With this review, we aim to summarize the most notable results in the field whilst encouraging further research to deal with the future challenges that animal production in the tropics will need to face.
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Affiliation(s)
- David M Ribeiro
- LEAF Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, Lisboa, Portugal
| | - Ahmed A K Salama
- Group of Research in Ruminants (G2R), Department of Animal and Food Science, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Ana C M Vitor
- CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. da Universidade Técnica, Lisboa, Portugal
| | - Anastasio Argüello
- Animal Production and Biotechnology group, Institute of Animal Health and Food Safety, Universidad de Las Palmas de Gran Canaria, 35413 Arucas, Spain
| | - Cristina T Moncau
- FZEA - Faculty of Animal Science and Food Engineering, University of São Paulo, Avenida Duque de Caxias Norte - 225, 13635-900 Pirassununga, SP, Brazil
| | - Edson M Santos
- Departamento de Zootecnia, Centro de Ciências Agrárias, Universidade Federal da Paraíba, Areia, PB, Brazil
| | - Gerardo Caja
- Group of Research in Ruminants (G2R), Department of Animal and Food Science, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Juliana S de Oliveira
- Departamento de Zootecnia, Centro de Ciências Agrárias, Universidade Federal da Paraíba, Areia, PB, Brazil
| | - Júlio C C Balieiro
- FMVZ - School of Veterinary Medicine and Animal Science, University of São Paulo, Avenida Duque de Caxias Norte - 225, 13635-900 Pirassununga, SP, Brazil
| | | | - Maya Zachut
- Department of Ruminant Science, Institute of Animal Sciences Agricultural Research Organization/Volcani Center, Rishon Lezion 7505101, Israel
| | - Mirele D Poleti
- FZEA - Faculty of Animal Science and Food Engineering, University of São Paulo, Avenida Duque de Caxias Norte - 225, 13635-900 Pirassununga, SP, Brazil
| | - Noemi Castro
- Animal Production and Biotechnology group, Institute of Animal Health and Food Safety, Universidad de Las Palmas de Gran Canaria, 35413 Arucas, Spain
| | - Susana P Alves
- CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. da Universidade Técnica, Lisboa, Portugal
| | - André M Almeida
- LEAF Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, Lisboa, Portugal.
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Wang M, Xie X, Wang M, Wu J, Zhou Q, Sun Y. The bacterial microbiota in florfenicol contaminated soils: The antibiotic resistome and the nitrogen cycle. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 259:113901. [PMID: 32023788 DOI: 10.1016/j.envpol.2019.113901] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/18/2019] [Accepted: 12/28/2019] [Indexed: 06/10/2023]
Abstract
Soil antibiotic resistome and the nitrogen cycle are affected by florfenicol addition to manured soils but their interactions have not been fully described. In the present study, antibiotic resistance genes (ARGs) and nitrogen cycle genes possessed by soil bacteria were characterized using real-time fluorescence quantification PCR (qPCR) and metagenomic sequencing in a short-term (30 d) soil model experiment. Florfenicol significantly changed in the abundance of genes conferring resistance to aminoglycosides, β-lactams, tetracyclines and macrolides. And the abundance of Sphingomonadaceae, the protein metabolic and nitrogen metabolic functions, as well as NO reductase, nitrate reductase, nitrite reductase and N2O reductase can also be affected by florfenicol. In this way, ARG types of genes conferring resistance to aminoglycosides, β-lactamases, tetracyclines, colistin, fosfomycin, phenicols and trimethoprim were closely associated with multiple nitrogen cycle genes. Actinobacteria, Chlorobi, Firmicutes, Gemmatimonadetes, Nitrospirae, Proteobacteria and Verrucomicrobia played an important role in spreading of ARGs. Moreover, soil physicochemical properties were important factors affecting the distribution of soil flora. This study provides a theoretical basis for further exploration of the transmission regularity and interference mechanism of ARGs in soil bacteria responsible for nitrogen cycle.
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Affiliation(s)
- Mei Wang
- The Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Xiying Xie
- The Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Mianzhi Wang
- The Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Jing Wu
- The Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Qin Zhou
- The Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Yongxue Sun
- The Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China.
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Rathod MG, Pathak AP. Wealth from waste: Optimized alkaline protease production from agro-industrial residues by Bacillus alcalophilus LW8 and its biotechnological applications. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2018. [DOI: 10.1016/j.jtusci.2014.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Mukundraj G. Rathod
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Dnyanteerth, Vishnupuri, Nanded 431606, India
| | - Anupama P. Pathak
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Dnyanteerth, Vishnupuri, Nanded 431606, India
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High diversity and abundance of cultivable tetracycline-resistant bacteria in soil following pig manure application. Sci Rep 2018; 8:1489. [PMID: 29367695 PMCID: PMC5784163 DOI: 10.1038/s41598-018-20050-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/12/2018] [Indexed: 11/13/2022] Open
Abstract
By performing a microcosm experiment mimicking fertilization, we assessed the dynamic distribution of tetracycline-resistant bacteria (TRB) and corresponding tetracycline resistance genes (TRGs) from pig manure (PM) to the fertilized soil, by culture-dependent methods and PCR detection. Cultivable TRB were most abundant in PM, followed by fertilized soil and unfertilized soil. By restriction fragment length polymorphism (RFLP) analysis, TRB were assigned to 29, 20, and 153 operational taxonomic units (OTUs) in PM, unfertilized soil, and fertilized soil, respectively. After identification, they were further grouped into 19, 12, and 62 species, showing an enhanced diversity of cultivable TRB in the soil following PM application. The proportions of potentially pathogenic TRB in fertilized soil decreased by 69.35% and 41.92% compared with PM and unfertilized soil. Bacillus cereus was likely widely distributed TRB under various environments, and Rhodococcus erythropolis and Acinetobacter sp. probably spread from PM to the soil via fertilization. Meanwhile, tetL was the most common efflux pump gene in both unfertilized and fertilized soils relative to PM; tetB(P) and tet36 were common in PM, whereas tetO was predominant in unfertilized and fertilized soil samples. Sequencing indicated that over 65% of randomly selected TRB in fertilized soil with acquired resistance derived from PM.
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Kang Y, Li Q, Xia D, Shen M, Mei L, Hu J. Short-term thermophilic treatment cannot remove tetracycline resistance genes in pig manures but exhibits controlling effects on their accumulation and spread in soil. JOURNAL OF HAZARDOUS MATERIALS 2017; 340:213-220. [PMID: 28715744 DOI: 10.1016/j.jhazmat.2017.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/21/2017] [Accepted: 07/06/2017] [Indexed: 06/07/2023]
Abstract
In this work, a microcosm experiment was conducted to merely mimic thermophilic phase in aerobic composting with pig manures in order to explore: (i) the effect of thermophilic phase in composting on the abundances of tetracycline resistance genes (TRGs); and (ii) the impacts of the treated manures on the abundances of TRGs in soil. It was found that 4days of thermophilic process reduced the abundance of TRGs in pig manures by ∼1 lg unit compared to the samples without treatments, suggesting that other phases in composting may play significant roles in removal of TRGs. Once pig manures with thermophilic treatment were applied to soil, TRGs abundances decreased to the levels in unfertilized soil. With correlation analyses, it was concluded that pig manure derived tetracycline-resistant bacteria (TRB) and nutrients exerted different effects on TRGs abundances in soil. In conclusion, short-term thermophilic treatment cannot remove tetracycline resistance genes in pig manures but exhibits controlling effects on their accumulation and spread in soil. Nutrients enrichment in soil following manuring of treated pig manures, together with a large proportion of gram-positive TRB left in treated pig manures with less risk to TRGs spread, contributed to the controlling effects.
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Affiliation(s)
- Yijun Kang
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, PR China; College of Marine and Bio-Engineering, Yancheng Teachers University, Yancheng, Jiangsu, PR China.
| | - Qing Li
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Dan Xia
- College of Marine and Bio-Engineering, Yancheng Teachers University, Yancheng, Jiangsu, PR China
| | - Min Shen
- College of Marine and Bio-Engineering, Yancheng Teachers University, Yancheng, Jiangsu, PR China
| | - Lijuan Mei
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Jian Hu
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, PR China; Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, Jiangsu, PR China.
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11
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Abstract
Lake Meyghan is one of the largest and commercially most important salt lakes in Iran. Despite its inland location and high altitude, Lake Meyghan has a thalassohaline salt composition suggesting a marine origin. Inputs of fresh water by rivers and rainfall formed various basins characterized by different salinities. We analyzed the microbial community composition of three basins by isolation and culturing of microorganisms and by analysis of the metagenome. The basins that were investigated comprised a green ~50 g kg−1 salinity brine, a red ~180 g kg−1 salinity brine and a white ~300 g kg−1 salinity brine. Using different growth media, 57 strains of Bacteria and 48 strains of Archaea were isolated. Two bacterial isolates represent potential novel species with less than 96% 16S rRNA gene sequence identity to known species. Abundant isolates were also well represented in the metagenome. Bacteria dominated the low salinity brine, with Alteromonadales (Gammaproteobacteria) as a particularly important taxon, whereas the high salinity brines were dominated by haloarchaea. Although the brines of Lake Meyghan differ in geochemical composition, their ecosystem function appears largely conserved amongst each other while being driven by different microbial communities.
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Sinha SK, Chaturvedi VB, Singh P, Chaudhary LC, Ghosh M, Shivani S. Effect of high and low roughage total mixed ration diets on rumen metabolites and enzymatic profiles in crossbred cattle and buffaloes. Vet World 2017; 10:616-622. [PMID: 28717312 PMCID: PMC5499077 DOI: 10.14202/vetworld.2017.616-622] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 04/19/2017] [Indexed: 11/30/2022] Open
Abstract
Aim:: A comparative study was conducted on crossbred cattle and buffaloes to investigate the effect of feeding high and low roughage total mixed ration (TMR) diets on rumen metabolites and enzymatic profiles. Materials and Methods:: Three rumen-fistulated crossbred cattle and buffalo were randomly assigned as per 3×3 switch over design for 21-days. Three TMR diets consisting of concentrate mixture, wheat straw and green maize fodder in the ratios of (T1) 60:20:20, (T2) 40:30:30, and (T3) 20:40:40, respectively, were fed to the animals ad libitum. Rumen liquor samples were collected at 0, 2, 4, 6, and 8 h post feeding for the estimation of rumen biochemical parameters on 2 consecutive days in each trial. Results:: The lactic acid concentration and pH value were comparable in both species and treatments. Feed intake (99.77±2.51 g/kg body weight), ruminal ammonia nitrogen, and total nitrogen were significantly (p<0.05) higher in buffalo and in treatment group fed with high concentrate diet. Production of total volatile fatty acids (VFAs) was non-significant (p>0.05) among treatments and significantly (p<0.05) greater in crossbred cattle than buffaloes. Molar proportions of individual VFAs propionate (C3), propionate:butyrate (C3:C4), and (acetate+butyrate):propionate ([C2+C4]:C3) ratio in both crossbred cattle and buffalo were not affected by high or low roughage diet, but percentage of acetate and butyrate varied significantly (p<0.05) among treatment groups. Activities of microbial enzymes were comparable among species and different treatment groups. A total number of rumen protozoa were significantly (p<0.05) higher in crossbred cattle than buffaloes along with significantly (p<0.05) higher population in animal fed with high concentrate diet (T1). Conclusion:: Rumen microbial population and fermentation depend on constituents of the treatment diet. However, microbial enzyme activity remains similar among species and different treatments. High concentrate diet increases number of rumen protozoa, and the number is higher in crossbred cattle than buffaloes.
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Affiliation(s)
- S K Sinha
- Division of Animal Nutrition, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly - 243 122, Uttar Pradesh, India.,Department of Animal Nutrition, Ranchi Veterinary College, Birsa Agricultural University, Kanke, Ranchi - 834 006, Jharkhand, India
| | - V B Chaturvedi
- Division of Animal Nutrition, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly - 243 122, Uttar Pradesh, India
| | - Putan Singh
- Division of Animal Nutrition, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly - 243 122, Uttar Pradesh, India
| | - L C Chaudhary
- Division of Animal Nutrition, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly - 243 122, Uttar Pradesh, India
| | - Mayukh Ghosh
- Department of Veterinary Biochemistry, Ranchi Veterinary College, Birsa Agricultural University, Kanke, Ranchi - 834 006, Jharkhand, India
| | - Swati Shivani
- Division of Animal Nutrition, ICAR-National Dairy Research Institute, Karnal - 132 001, Haryana, India
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Generation and Characterization of Acid Tolerant Fibrobacter succinogenes S85. Sci Rep 2017; 7:2277. [PMID: 28536480 PMCID: PMC5442110 DOI: 10.1038/s41598-017-02628-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 04/20/2017] [Indexed: 01/13/2023] Open
Abstract
Microorganisms are key components for plant biomass breakdown within rumen environments. Fibrobacter succinogenes have been identified as being active and dominant cellulolytic members of the rumen. In this study, F. succinogenes type strain S85 was adapted for steady state growth in continuous culture at pH 5.75 and confirmed to grow in the range of pH 5.60–5.65, which is lower than has been reported previously. Wild type and acid tolerant strains digested corn stover with equal efficiency in batch culture at low pH. RNA-seq analysis revealed 268 and 829 genes were differentially expressed at pH 6.10 and 5.65 compared to pH 6.70, respectively. Resequencing analysis identified seven single nucleotide polymorphisms (SNPs) in the sufD, yidE, xylE, rlmM, mscL and dosC genes of acid tolerant strains. Due to the absence of a F. succinogenes genetic system, homologues in Escherichia coli were mutated and complemented and the resulting strains were assayed for acid survival. Complementation with wild-type or acid tolerant F. succinogenes sufD restored E. coli wild-type levels of acid tolerance, suggesting a possible role in acid homeostasis. Recent genetic engineering developments need to be adapted and applied in F. succinogenes to further our understanding of this bacterium.
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14
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Hinsu AT, Parmar NR, Nathani NM, Pandit RJ, Patel AB, Patel AK, Joshi CG. Functional gene profiling through metaRNAseq approach reveals diet-dependent variation in rumen microbiota of buffalo (Bubalus bubalis). Anaerobe 2017; 44:106-116. [PMID: 28246035 DOI: 10.1016/j.anaerobe.2017.02.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 02/18/2017] [Accepted: 02/23/2017] [Indexed: 10/20/2022]
Abstract
Recent advances in next generation sequencing technology have enabled analysis of complex microbial community from genome to transcriptome level. In the present study, metatranscriptomic approach was applied to elucidate functionally active bacteria and their biological processes in rumen of buffalo (Bubalus bubalis) adapted to different dietary treatments. Buffaloes were adapted to a diet containing 50:50, 75:25 and 100:0 forage to concentrate ratio, each for 6 weeks, before ruminal content sample collection. Metatranscriptomes from rumen fiber adherent and fiber-free active bacteria were sequenced using Ion Torrent PGM platform followed by annotation using MG-RAST server and CAZYmes (Carbohydrate active enzymes) analysis toolkit. In all the samples Bacteroidetes was the most abundant phylum followed by Firmicutes. Functional analysis using KEGG Orthology database revealed Metabolism as the most abundant category at level 1 within which Carbohydrate metabolism was dominating. Diet treatments also exerted significant differences in proportion of enzymes involved in metabolic pathways for VFA production. Carbohydrate Active Enzyme(CAZy) analysis revealed the abundance of genes encoding glycoside hydrolases with the highest representation of GH13 CAZy family in all the samples. The findings provide an overview of the activities occurring in the rumen as well as active bacterial population and the changes occurring through different dietary treatments.
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Affiliation(s)
- Ankit T Hinsu
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India
| | - Nidhi R Parmar
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India
| | - Neelam M Nathani
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India
| | - Ramesh J Pandit
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India
| | - Anand B Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India
| | - Amrutlal K Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University (AAU), Anand, Gujarat, India.
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15
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Kang Y, Hao Y, Xia D, Shen M, Li Q, Hu J. The effects of pig manure application on the spread of tetracycline resistance in bulk and cucumber rhizosphere soils: a greenhouse experiment. Can J Microbiol 2017; 63:563-572. [PMID: 28222270 DOI: 10.1139/cjm-2016-0767] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
It is important to understand the dynamics of tetracycline-resistant bacteria (TRB) and tetracycline resistance genes (TRGs) in bulk and rhizosphere soils for evaluating the spread of TRGs from pig manure to human. In this work, a greenhouse experiment was conducted to investigate the difference in abundance of TRB, tetracycline-resistant Escherichia coli (TRE), tetracycline-resistant Pseudomonas spp. (TRP), and TRGs between bulk and cucumber rhizosphere soils. The application of pig manure resulted in the long-term persistence of TRB, TRE, TRP, and TRGs in bulk soil and rhizosphere of cucumber for at least 65 days. Pig manure application dose was the major driving force in altering the abundances of TRB and TRE, whereas TRP was disturbed mainly by compartment (bulk soil or rhizosphere). Both TRE and the percentage of TRE in bulk and rhizosphere soils increased linearly with an increase in dose of pig manure. The exponential relationships between pig manure dose and TRP along with TRP percentage were also noted. There were significant differences in the relative abundances of TRGs between bulk and cucumber rhizosphere soils, suggesting the use of pig manure exerted a more lasting impact on the spread of TRGs in the rhizosphere than in the bulk soil.
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Affiliation(s)
- Yijun Kang
- a Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, People's Republic of China.,b College of Marine and Bio-engineering, Yancheng Teachers University, Yancheng, Jiangsu, People's Republic of China
| | - Yangyang Hao
- a Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, People's Republic of China
| | - Dan Xia
- b College of Marine and Bio-engineering, Yancheng Teachers University, Yancheng, Jiangsu, People's Republic of China
| | - Min Shen
- b College of Marine and Bio-engineering, Yancheng Teachers University, Yancheng, Jiangsu, People's Republic of China
| | - Qing Li
- a Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, People's Republic of China
| | - Jian Hu
- a Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, People's Republic of China
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16
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Kang Y, Hao Y, Shen M, Zhao Q, Li Q, Hu J. Impacts of supplementing chemical fertilizers with organic fertilizers manufactured using pig manure as a substrate on the spread of tetracycline resistance genes in soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2016; 130:279-288. [PMID: 27152658 DOI: 10.1016/j.ecoenv.2016.04.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 04/15/2016] [Accepted: 04/23/2016] [Indexed: 06/05/2023]
Abstract
Using pig manure (PM) compost as a partial substitute for the conventional chemical fertilizers (CFs) is considered an effective approach in sustainable agricultural systems. This study aimed to analyze the impacts of supplementing CF with organic fertilizers (OFs) manufactured using pig manure as a substrate on the spread of tetracycline resistance genes (TRGs) as well as the community structures and diversities of tetracycline-resistant bacteria (TRB) in bulk and cucumber rhizosphere soils. In this study, three organic fertilizers manufactured using the PM as a substrate, namely fresh PM, common OF, and bio-organic fertilizer (BF), were supplemented with a CF. Composted manures combined with a CF did not significantly increase TRB compared with the CF alone, but PM treatment resulted in the long-term survival of TRB in soil. The use of CF+PM also increased the risk of spreading TRGs in soil. As beneficial microorganisms in BF may function as reservoirs for the spread of antibiotic resistance genes, care should be taken when adding them to the OF matrix. The PM treatment significantly altered the community structures and increased the species diversity of TRB, especially in the rhizosphere soil. BF treatment caused insignificant changes in the community structure of TRB compared with CF treatment, yet it reduced the species diversities of TRB in soil. Thus, the partial use of fresh PM as a substitute for CF could increase the risk of spread of TRGs. Apart from plant growth promotion, BF was a promising fertilizer owing to its potential ability to control TRGs.
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Affiliation(s)
- Yijun Kang
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, PR China; College of Marine and Bio-engineering, Yancheng Teachers University, Yancheng, Jiangsu, PR China
| | - Yangyang Hao
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Min Shen
- College of Marine and Bio-engineering, Yancheng Teachers University, Yancheng, Jiangsu, PR China
| | - Qingxin Zhao
- College of Marine and Bio-engineering, Yancheng Teachers University, Yancheng, Jiangsu, PR China
| | - Qing Li
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Jian Hu
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, PR China.
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17
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Sun H, Ni X, Song X, Wen B, Zhou Y, Zou F, Yang M, Peng Z, Zhu H, Zeng Y, Wang H, Fu X, Shi Y, Yin Z, Pan K, Jing B, Zeng D, Wang P. Fermented Yupingfeng polysaccharides enhance immunity by improving the foregut microflora and intestinal barrier in weaning rex rabbits. Appl Microbiol Biotechnol 2016; 100:8105-20. [DOI: 10.1007/s00253-016-7619-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 05/01/2016] [Accepted: 05/07/2016] [Indexed: 02/06/2023]
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18
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Franzolin R, Wright ADG. Microorganisms in the rumen and reticulum of buffalo (Bubalus bubalis) fed two different feeding systems. BMC Res Notes 2016; 9:243. [PMID: 27118203 PMCID: PMC4847366 DOI: 10.1186/s13104-016-2046-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 04/15/2016] [Indexed: 11/10/2022] Open
Abstract
Background The community of microorganisms in the rumen and reticulum is influenced by feeding as well as the species and geographical distribution of ruminant animals. Bacteria, methanogenic archaea and ciliate protozoa existing in the rumen and reticulum were evaluated by real-time polymerase chain reaction and light microscopy in buffalo in two feeding systems, grazing and feedlot. Results No significant differences were observed in the total concentrations of bacteria/mL and archaea between rumen and reticulum, and between pasture and feedlots, or interactions between variables. However, the largest density of bacteria and smallest density of archaea was observed in the rumen of grazing animals. The total ciliates protozoa community was higher in grazing buffalo than those in the feedlot on a concentrated diet. There were significant interactions between location in the gastrointestinal tract (rumen vs reticulum) and types of diets (grazing vs feedlot) in the composition of ciliates. Conclusions Our data showed differences in the microbial community of the rumen and reticulum between grazing and feedlot feeding systems demonstrating relevant changes in the microorganism:host relationship existing on rumen–reticulum ecosystem.
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Affiliation(s)
- Raul Franzolin
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP, 13630900, Brazil
| | - André-Denis G Wright
- School of Animal and Comparative Biomedical Sciences, College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ, 85721, USA.
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19
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Nathani NM, Kothari RK, Patel AK, Joshi CG. Functional Characterization Reveals Novel Putative Coding Sequences in Prevotella ruminicola Genome Extracted from Rumen Metagenomic Studies. J Mol Microbiol Biotechnol 2015; 25:292-9. [PMID: 26304839 DOI: 10.1159/000437265] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
AIM To reassemble Prevotella ruminicola genome from rumen metagenomic data of cattle and buffalo and compare with the published reference genome. METHOD Rumen microbial communities from Mehsani buffaloes (n = 8) and Kankrej cattle (n = 8), each adapted to different proportions of a dry or green roughage diet, were subjected to metagenomic sequencing by Ion Torrent PGM, and subsequent reads were analyzed by MG-RAST. Using reference-guided assembly of the sequences against the published P. ruminicola strain 23, draft genomes of 2.56 and 2.46 Mb were reconstructed from Mehsani buffalo and Kankrej cows, respectively. The genomes were annotated using the RAST Server and carbohydrate active enzyme (CAZyme) analysis. RESULTS Taxonomic analysis by MG-RAST revealed P. ruminicola to be the most abundant species present among the rumen microflora. Functional annotation of reconstructed genomes using the RAST Server depicted the maximum assignment of coding sequences involved in the subsystems amino acid and derivatives and carbohydrate metabolism. CAZyme profiling revealed the glycoside hydrolases (GH) family to be the most abundant. GH family subclassification revealed that the extracted genomes had more sequence hits for GH2, GH3, GH92 and GH97 as compared to the reference. CONCLUSION The results reflect the metabolic significance of rumen-adapted P. ruminicola in utilizing a coarse diet for animals based on acquisition of novel genetic elements.
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Singh KM, Jisha TK, Reddy B, Parmar N, Patel A, Patel AK, Joshi CG. Microbial profiles of liquid and solid fraction associated biomaterial in buffalo rumen fed green and dry roughage diets by tagged 16S rRNA gene pyrosequencing. Mol Biol Rep 2014; 42:95-103. [PMID: 25249226 DOI: 10.1007/s11033-014-3746-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 09/16/2014] [Indexed: 02/06/2023]
Abstract
The microbiome of buffalo rumen plays an important role in animal health and productivity. The rumen bacterial composition of both liquid and solid fraction was surveyed using pyrosequencing of the 16S rRNA gene. Sequences were analyzed using taxonomy-dependent clustering methods and revealed that the dominant ruminal bacteria shared by samples belonged to phyla Bacteroidetes, Firmicutes, Fibrobacteres and Proteobacteria. The core rumen microbiome of the rumen consisted of 10 phyla, 19 classes, 22 orders and 25 families. However, the relative abundance of these bacterial groups was markedly affected by diet composition as well as in type of biomaterial. In animals fed with a green and dry roughage diet, the cellulolytic bacteria, Ruminococcaceae, and Fibrobacteraceae was found in highest abundance in all biomaterials which reflected the need for enhanced fiber-digesting capacity in buffalo. The polysaccharide-degrading Prevotellaceae bacteria were most abundant in buffalo rumen. In taxonomic comparison of rumen bacteria, about 26 genera were differentially abundant among liquid and solid fraction of ruminal fluid. These results highlight the buffalo ruminal microbiome's ability to adapt to feed with different composition.
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Affiliation(s)
- K M Singh
- Department of Animal Biotechnology, Anand Agricultural University, Anand, India,
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21
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Abstract
Summary: The development of bioinformatic solutions for microbial ecology in Perl is limited by the lack of modules to represent and manipulate microbial community profiles from amplicon and meta-omics studies. Here we introduce Bio-Community, an open-source, collaborative toolkit that extends BioPerl. Bio-Community interfaces with commonly used programs using various file formats, including BIOM, and provides operations such as rarefaction and taxonomic summaries. Bio-Community will help bioinformaticians to quickly piece together custom analysis pipelines and develop novel software. Availability an implementation: Bio-Community is cross-platform Perl code available from http://search.cpan.org/dist/Bio-Community under the Perl license. A readme file describes software installation and how to contribute. Contact:f.angly@uq.edu.au Supplementary information:Supplementary data are available at Bioinformatics online
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Affiliation(s)
- Florent E Angly
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, Level 5, Molecular Biosciences Building (76), The University of Queensland, Brisbane St Lucia, QLD 4072, Australia and HPCBio, Carver Biotechnology Center, Institute for Genomic Biology, 1206 West Gregory Drive
- MC-195, Urbana, IL 61801, USA
| | - Christopher J Fields
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, Level 5, Molecular Biosciences Building (76), The University of Queensland, Brisbane St Lucia, QLD 4072, Australia and HPCBio, Carver Biotechnology Center, Institute for Genomic Biology, 1206 West Gregory Drive
- MC-195, Urbana, IL 61801, USA
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, Level 5, Molecular Biosciences Building (76), The University of Queensland, Brisbane St Lucia, QLD 4072, Australia and HPCBio, Carver Biotechnology Center, Institute for Genomic Biology, 1206 West Gregory Drive
- MC-195, Urbana, IL 61801, USA
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