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Selected Alternative Feed Additives Used to Manipulate the Rumen Microbiome. Animals (Basel) 2021; 11:ani11061542. [PMID: 34070442 PMCID: PMC8228006 DOI: 10.3390/ani11061542] [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] [Received: 05/03/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 12/23/2022] Open
Abstract
Simple Summary The continuous intensification of ruminant production drives towards the expansion of feed components and additives that are utilizes for the coverage of animal’s demand for nutrients. Additionally, in recent years, studies are focused on the investigation of how feed additives affect the microbiome of the digestive system in order to obtain improved performance and/or reduce methane emissions by ruminants. The use of additives such as algae, probiotics, fermented feed or essential oils can serve as an alternative to antibiotics or other synthetic compounds that may pose a danger to the environment. Abstract In recent years, a boost in the ruminant population has been observed, and consequently, an increase in the animals’ demand for nutrients and methane emissions. Methane emission is generated during the microbial fermentation of feed in the rumen, and a percentage even up to 12% of the energy obtained by this process can be wasted. In addition, the use of antibiotics in animal husbandry is being increasingly restricted. restricted. As a result, there is a continuous search for innovative feed additives that can serve as alternatives to antibiotics, and will also be safe for both people and the environment. In the present review article, additives were selected on basis that, according to studies conducted so far, may positively affect the microbiome of the digestive system by improving indicators and/or reducing methane production. Among them, probiotics, prebiotics or their combination—synbiotics are at the forefront of research. However, additives in the form of algae or plant origin are also gaining ground in popularity, such as essential oils, fermented wheat straw or Gelidium amansii, due to their general recognition as safe (GRAS) for both humans and environment.
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Molina NM, Sola-Leyva A, Haahr T, Aghajanova L, Laudanski P, Castilla JA, Altmäe S. Analysing endometrial microbiome: methodological considerations and recommendations for good practice. Hum Reprod 2021; 36:859-879. [DOI: 10.1093/humrep/deab009] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/02/2020] [Indexed: 12/12/2022] Open
Abstract
ABSTRACT
There is growing evidence that the upper female genital tract is not sterile, harbouring its own microbial communities. However, the significance and the potential effect of endometrial microorganisms on reproductive functions remain to be fully elucidated. Analysing the endometrial microbiome, the microbes and their genetic material present in the endometrium, is an emerging area of study. The initial studies suggest it is associated with poor reproductive outcomes and with different gynaecological pathologies. Nevertheless, studying a low-biomass microbial niche as is endometrium, the challenge is to conduct well-designed and well-controlled experiments in order to avoid and adjust for the risk of contamination, especially from the lower genital tract. Herein, we aim to highlight methodological considerations and propose good practice recommendations for future endometrial microbiome studies.
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Affiliation(s)
- Nerea M Molina
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada 18071, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
| | - Alberto Sola-Leyva
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada 18071, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
| | - Thor Haahr
- The Fertility Clinic, Skive Regional Hospital, Skive 7800, Denmark
| | - Lusine Aghajanova
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Stanford School of Medicine, Sunnyvale, CA 94087, USA
| | - Piotr Laudanski
- Department of Obstetrics and Gynecology, Medical University of Warsaw, Warsaw 02-015, Poland
| | - Jose Antonio Castilla
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
- Unidad de Reproducción, UGC de Obstetricia y Ginecología, Hospital Universitario Virgen de las Nieves, Granada 18012, Spain
- CEIFER Biobanco—NextClinics, Granada 18004, Spain
| | - Signe Altmäe
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada 18071, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
- Competence Centre on Health Technologies, Tartu 50410, Estonia
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Zhang J, Liu YX, Guo X, Qin Y, Garrido-Oter R, Schulze-Lefert P, Bai Y. High-throughput cultivation and identification of bacteria from the plant root microbiota. Nat Protoc 2021; 16:988-1012. [PMID: 33442053 DOI: 10.1038/s41596-020-00444-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 10/13/2020] [Indexed: 01/29/2023]
Abstract
Cultivating native bacteria from roots of plants grown in a given environment is essential for dissecting the functions of the root microbiota for plant growth and health with strain-specific resolution. In this study, we established a straightforward protocol for high-throughput bacterial isolation from fresh root samples using limiting dilution to ensure that most cultured bacteria originated from only one microorganism. This is followed by strain characterization using a two-sided barcode polymerase chain reaction system to identify pure and heterogeneous bacterial cultures. Our approach overcomes multiple difficulties of traditional bacterial isolation and identification methods, such as obtaining bacteria with diverse growth rates while greatly increasing throughput. To facilitate data processing, we developed an easy-to-use bioinformatic pipeline called 'Culturome' ( https://github.com/YongxinLiu/Culturome ) and a graphical user interface web server ( http://bailab.genetics.ac.cn/culturome/ ). This protocol allows any research group (two or three lab members without expertise in bioinformatics) to systematically cultivate root-associated bacteria within 8-9 weeks.
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Affiliation(s)
- Jingying Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.,CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yong-Xin Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.,CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoxuan Guo
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.,CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yuan Qin
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.,CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ruben Garrido-Oter
- Max Planck Institute for Plant Breeding Research, Cologne, Germany. .,Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany.
| | - Paul Schulze-Lefert
- Max Planck Institute for Plant Breeding Research, Cologne, Germany. .,Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany.
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China. .,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China. .,CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. .,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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