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Abdullah HM, Mohammed OB, Sheikh A, Almathen F, Khalid AM, Bakhiet AO, Abdelrahman MM. Molecular detection of ruminal micro-flora and micro-fauna in Saudi Arabian camels: Effects of season and region. Saudi J Biol Sci 2024; 31:103982. [PMID: 38600912 PMCID: PMC11004988 DOI: 10.1016/j.sjbs.2024.103982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/12/2024] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
This study investigated and explored the availability of micro-flora and micro-fauna in the ruminal contents of Arabian camel (Camelus dromedarius) from three different regions in Saudi Arabia along with two seasons. Samples were prepared and tested by conventional polymerase chain reaction (PCR). This study confirmed that the bacterial flora were dominating over other microbes. Different results of the availability of each microbe in each region and season were statistically analyzed and discussed. There was no significant effect of season on the micro-flora or micro-fauna however, the location revealed a positive effect with Ruminococcus flavefaciens (p < 0 0.03) in the eastern region. This study was the first to investigate the abundance of micro-flora and micro-fauna in the ruminal contents of camels of Saudi Arabia. This study underscores the significance of camel ruminal micro-flora and micro-fauna abundance, highlighting their correlation with both seasonality and geographic location. This exploration enhances our comprehension of camel rumination and digestion processes. The initial identification of these microbial communities serves as a foundational step, laying the groundwork for future in-depth investigations into camel digestibility and nutritional requirements.
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Affiliation(s)
- Hashim M. Abdullah
- Camel Research Center, King Faisal University, P.O. Box 400, Al-Hofuf 31982, Al-Ahsa, Saudi Arabia
| | - Osama B. Mohammed
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah Sheikh
- Camel Research Center, King Faisal University, P.O. Box 400, Al-Hofuf 31982, Al-Ahsa, Saudi Arabia
| | - Faisal Almathen
- Camel Research Center, King Faisal University, P.O. Box 400, Al-Hofuf 31982, Al-Ahsa, Saudi Arabia
- Department of Veterinary Public Health, College of Veterinary Medicine, King Faisal University, P.O. Box 400, Al-Hofuf 31982, Al-Ahsa, Saudi Arabia
| | - Ahmed M. Khalid
- Department of Veterinary Public Health, College of Veterinary Medicine, King Faisal University, P.O. Box 400, Al-Hofuf 31982, Al-Ahsa, Saudi Arabia
- Department of Genetics and Animal Breeding, Faculty of Animal Production, University of Khartoum, Shambat 13314, Sudan
| | - Amel O. Bakhiet
- Deanship of Scientific Research, Sudan University of Science and Technology, P.O. Box 407, Khartoum, Sudan
| | - Mutassim M. Abdelrahman
- Department of Animal Production, College of Food and Agriculture Science, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
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Guo W, Liu T, Neves ALA, Long R, Degen A, Zhou M, Chen X. Transmission of fungi and protozoa under grazing conditions from lactating yaks to sucking yak calves in early life. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12616-y. [PMID: 37341753 DOI: 10.1007/s00253-023-12616-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/22/2023]
Abstract
Microbiota from mothers is an essential source of microbes in early-life rumen microbiota, but the contribution of microbiota from different maternal sites to the rumen microbiota establishment in neonates needs more data. To fill this gap, we collected samples from the mouth, teat skin, and rumen of lactating yaks and from the rumen of sucking calves concomitantly on seven occasions between days 7 and 180 after birth under grazing conditions. We observed that the eukaryotic communities clustered based on sample sites, except for the protozoal community in the teat skin, with negative correlations between fungal and protozoal diversities in the rumen of calves. Furthermore, fungi in the dam's mouth, which is the greatest source of the calf's rumen fungi, accounted for only 0.1%, and the contribution of the dam's rumen to the calf's rumen fungi decreased with age and even disappeared after day 60. In contrast, the average contribution of the dam's rumen protozoa to the calf's rumen protozoa was 3.7%, and the contributions from the dam's teat skin (from 0.7 to 2.7%) and mouth (from 0.4 to 3.3%) increased with age. Thus, the divergence in dam-to-calf transmissibility between fungi and protozoa indicates that the foundation of these eukaryotic communities is shaped by different rules. This study provides the first measurements of the maternal contribution to the fungal and protozoal establishment in the rumen of sucking and grazing yak calves in early life, which could be beneficial for future microbiota manipulation in neonatal ruminants. KEY POINTS: • Dam to calf transfer of rumen eukaryotes occurs from multiple body sites. • A minor proportion of rumen fungi in calves originated from maternal sites. • The inter-generation transmission between rumen fungi and protozoa differs.
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Affiliation(s)
- Wei Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, China
- State Key Laboratory of Grassland Agro-Ecosystems, International Centre of Tibetan Plateau Ecosystem Management, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- Department of Agricultural, Food and Nutritional Science, University of Alberta, EdmontonAlberta, AB, T6G 2P5, Canada
| | - Tingmei Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - André Luis Alves Neves
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 3, 1870, Frederiksberg C, Denmark
| | - Ruijun Long
- State Key Laboratory of Grassland Agro-Ecosystems, International Centre of Tibetan Plateau Ecosystem Management, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Allan Degen
- Desert Animal Adaptations and Husbandry, Wyler Department of Dryland Agriculture, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 8410500, Beer Sheva, Israel
| | - Mi Zhou
- Department of Agricultural, Food and Nutritional Science, University of Alberta, EdmontonAlberta, AB, T6G 2P5, Canada.
| | - Xiang Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, China.
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Elbir H, Alhumam NA. Sex Differences in Fecal Microbiome Composition and Function of Dromedary Camels in Saudi Arabia. Animals (Basel) 2022; 12:3430. [PMID: 36496952 PMCID: PMC9736497 DOI: 10.3390/ani12233430] [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] [Received: 09/27/2022] [Revised: 11/17/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The gastrointestinal microbiome plays a significant role in diet digestion and the energy production of its host. Several factors that affect the gastrointestinal microbiota composition were studied in camels. Yet, the impact of sex on the gastrointestinal bacteriome of camels remains unexplored to date. In this perspective, the fecal microbiome community composition from dromedary camels was determined in 10 male and 10 female samples using the 16S rRNA amplicon, in order to estimate if this was influenced by sex. The core microbiome in females contained 284 bacterial OTUs and one archaeal OUT, whereas in males, it contained 279 bacterial OTUs and one archaeal OTU. In females, Bacteroidetes and Spirochaetes were significantly more abundant than in male camels, whereas Lentisphaerae and Euryarchaeota were significantly abundant in males. According to Principal Coordinate Analysis and UPGMA clustering, grouping with respect to sex was observed. The functional prediction results showed differences such as energy production and conversion, and that the cell wall/membrane/envelope were enriched in female camels. The fecal microbiome of male camels was rich in amino acid, lipid transport and metabolism.
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Affiliation(s)
- Haitham Elbir
- Camel Research Center, King Faisal University, P.O. Box 400, Al-Hasa 31982, Saudi Arabia
| | - Naser Abdullah Alhumam
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, P.O. Box 400, Al-Hasa 31982, Saudi Arabia
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Joshi A, Young D, Huang L, Mosberger L, Munk B, Vinzelj J, Flad V, Sczyrba A, Griffith GW, Podmirseg SM, Warthmann R, Lebuhn M, Insam H. Effect of Growth Media on the Diversity of Neocallimastigomycetes from Non-Rumen Habitats. Microorganisms 2022; 10:1972. [PMID: 36296248 PMCID: PMC9612151 DOI: 10.3390/microorganisms10101972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/25/2022] [Accepted: 10/01/2022] [Indexed: 12/02/2022] Open
Abstract
Anaerobic fungi (AF), belonging to the phylum Neocallimastigomycota, are a pivotal component of the digestive tract microbiome of various herbivorous animals. In the last decade, the diversity of AF has rapidly expanded due to the exploration of numerous (novel) habitats. Studies aiming at understanding the role of AF require robust and reliable isolation and cultivation techniques, many of which remained unchanged for decades. Using amplicon sequencing, we compared three different media: medium with rumen fluid (RF), depleted rumen fluid (DRF), and no rumen fluid (NRF) to enrich the AF from the feces of yak, as a rumen control; and Przewalski's horse, llama, guanaco, and elephant, as a non-rumen habitats. The results revealed the selective enrichment of Piromyces and Neocallimastix from the feces of elephant and llama, respectively, in the RF medium. Similarly, the enrichment culture in DRF medium explicitly manifested Piromyces-related sequences from elephant feces. Five new clades (MM1-5) were defined from llama, guanaco, yak, and elephant feces that could as well be enriched from llama and elephant samples using non-conventional DRF and NRF media. This study presents evidence for the selective enrichment of certain genera in medium with RF and DRF from rumen as well as from non-rumen samples. NRF medium is suggested for the isolation of AF from non-rumen environments.
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Affiliation(s)
- Akshay Joshi
- Biocatalysis, Environment and Process Technology Unit, Life Science and Facility Management, Zurich University of Applied Sciences (ZHAW), 8820 Wadenswil, Switzerland
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25d, A-6020 Innsbruck, Austria
| | - Diana Young
- Central Department for Quality Assurance and Analytics, Micro- and Molecular Biology, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany
| | - Liren Huang
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Lona Mosberger
- Biocatalysis, Environment and Process Technology Unit, Life Science and Facility Management, Zurich University of Applied Sciences (ZHAW), 8820 Wadenswil, Switzerland
| | - Bernhard Munk
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Julia Vinzelj
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25d, A-6020 Innsbruck, Austria
| | - Veronika Flad
- Central Department for Quality Assurance and Analytics, Micro- and Molecular Biology, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany
| | - Alexander Sczyrba
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Gareth W. Griffith
- Department of Life Sciences, Cledwyn Building, Aberystwyth University, Aberystwyth SY23 3DD, UK
| | - Sabine Marie Podmirseg
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25d, A-6020 Innsbruck, Austria
| | - Rolf Warthmann
- Biocatalysis, Environment and Process Technology Unit, Life Science and Facility Management, Zurich University of Applied Sciences (ZHAW), 8820 Wadenswil, Switzerland
| | - Michael Lebuhn
- Central Department for Quality Assurance and Analytics, Micro- and Molecular Biology, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany
| | - Heribert Insam
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25d, A-6020 Innsbruck, Austria
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Xue Y, Shen R, Li Y, Sun Z, Sun X, Li F, Li X, Cheng Y, Zhu W. Anaerobic Fungi Isolated From Bactrian Camel Rumen Contents Have Strong Lignocellulosic Bioconversion Potential. Front Microbiol 2022; 13:888964. [PMID: 35928163 PMCID: PMC9345502 DOI: 10.3389/fmicb.2022.888964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/26/2022] [Indexed: 11/14/2022] Open
Abstract
This study aims to obtain anaerobic fungi from the rumen and fecal samples and investigates their potential for lignocellulosic bioconversion. Multiple anaerobic strains were isolated from rumen contents (CR1–CR21) and fecal samples (CF1–CF10) of Bactrian camel using the Hungate roll tube technique. After screening for fiber degradability, strains from rumen contents (Oontomyces sp. CR2) and feces (Piromyces sp. CF9) were compared with Pecoramyces sp. F1 (earlier isolated from goat rumen, having high CAZymes of GHs) for various fermentation and digestion parameters. The cultures were fermented with different substrates (reed, alfalfa stalk, Broussonetia papyrifera leaves, and Melilotus officinalis) at 39°C for 96 h. The Oontomyces sp. CR2 had the highest total gas and hydrogen production from most substrates in the in vitro rumen fermentation system and also had the highest digestion of dry matter, neutral detergent fiber, acid detergent fiber, and cellulose present in most substrates used. The isolated strains provided higher amounts of metabolites such as lactate, formate, acetate, and ethanol in the in vitro rumen fermentation system for use in various industrial applications. The results illustrated that anaerobic fungi isolated from Bactrian camel rumen contents (Oontomyces sp. CR2) have the highest lignocellulosic bioconversion potential, suggesting that the Bactrian camel rumen could be a good source for the isolation of anaerobic fungi for industrial applications.
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Affiliation(s)
- Yihan Xue
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Rui Shen
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Zhanying Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Xiaoni Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Fengming Li
- College of Animal Science, Xinjiang Agricultural University, Ürümqi, China
| | - Xiaobin Li
- College of Animal Science, Xinjiang Agricultural University, Ürümqi, China
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Yanfen Cheng,
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
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Ji Y, Dong X, Liu Z, Wang W, Yan H, Liu X. Effects of Bovine Pichia kudriavzevii T7, Candida glabrata B14, and Lactobacillus plantarum Y9 on Milk Production, Quality and Digestive Tract Microbiome in Dairy Cows. Microorganisms 2022; 10:842. [PMID: 35630288 PMCID: PMC9146454 DOI: 10.3390/microorganisms10050842] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 11/28/2022] Open
Abstract
Microbial administration has been used successfully to improve host health. However, the positive effects of endogenous microbials are still underexplored. This study investigated the effects of bovine Lactic acid bacteria and yeast on the milk production, quality and digestive tract microbiome of dairy cows. Lactobacillus plantarum Y9, Pichia kudriavzevii T7 and Candida glabrata B14 isolated from high-yielding dairy cows were selected to feed low-yielding Holstein cows. Pichia kudriavzevii T7 could significantly increase milk yield, meanwhile, Pichia kudriavzevii T7 and Candida glabrata B14 could obviously reduce the number of somatic cell counts (SCC). However, slight differences were found in milk fat, protein, lactose and SNF (solids not fat) percentage. High throughput sequencing showed that the dominant bacteria were Prevotella and Ruminococcaceae in rumen and feces, respectively, and the dominant fungi were Penicillium, Aspergillus and Trichoderma in both samples, before and after feeding the microbial addition. Nonetheless, microbial addition changed the abundance and structure of the microbiome in the digestive tract. Our data showed bovine yeast and LAB were beneficial for improving performance and regulating the microbial structure of dairy cows. This study was expected to enrich the knowledge of the digestive tract microbiome in dairy cows and provide a feasible strategy for the further utilization of bovine microorganisms.
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Affiliation(s)
| | | | | | | | - Hai Yan
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Y.J.); (X.D.); (Z.L.); (W.W.)
| | - Xiaolu Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Y.J.); (X.D.); (Z.L.); (W.W.)
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Ma J, Zhong P, Li Y, Sun Z, Sun X, Aung M, Hao L, Cheng Y, Zhu W. Hydrogenosome, Pairing Anaerobic Fungi and H 2-Utilizing Microorganisms Based on Metabolic Ties to Facilitate Biomass Utilization. J Fungi (Basel) 2022; 8:338. [PMID: 35448569 PMCID: PMC9026988 DOI: 10.3390/jof8040338] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 02/04/2023] Open
Abstract
Anaerobic fungi, though low in abundance in rumen, play an important role in the degradation of forage for herbivores. When only anaerobic fungi exist in the fermentation system, the continuous accumulation of metabolites (e.g., hydrogen (H2) and formate) generated from their special metabolic organelles-the hydrogenosome-inhibits the enzymatic reactions in the hydrogenosome and reduces the activity of the anaerobic fungi. However, due to interspecific H2 transfer, H2 produced by the hydrogenosome can be used by other microorganisms to form valued bioproducts. This symbiotic interaction between anaerobic fungi and other microorganisms can be used to improve the nutritional value of animal feeds and produce value-added products that are normally in low concentrations in the fermentation system. Because of the important role in the generation and further utilization of H2, the study of the hydrogensome is increasingly becoming an important part of the development of anaerobic fungi as model organisms that can effectively improve the utilization value of roughage. Here, we summarize and discuss the classification and the process of biomass degradation of anaerobic fungi and the metabolism and function of anaerobic fungal hydrogensome, with a focus on the potential role of the hydrogensome in the efficient utilization of biomass.
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Affiliation(s)
- Jing Ma
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
| | - Pei Zhong
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
| | - Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
| | - Zhanying Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
| | - Xiaoni Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
| | - Min Aung
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
- Department of Animal Nutrition, University of Veterinary Science, Nay Pyi Taw 15013, Myanmar
| | - Lizhuang Hao
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Plateau Yak Research Center, Qinghai Academy of Science and Veterinary Medicine of Qinghai University, Xining 810016, China;
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
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Rabee AE. Effect of barley straw and Egyptian clover hay on the rumen fermentation and structure and fibrolytic activities of rumen bacteria in dromedary camel. Vet World 2022; 15:35-45. [PMID: 35369587 PMCID: PMC8924375 DOI: 10.14202/vetworld.2022.35-45] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/17/2021] [Indexed: 01/04/2023] Open
Abstract
Background and Aim Understanding the regulations of rumen microbiota and their fibrolytic capabilities under different forages are essential to improve rumen fermentation and animal feed efficiency. This study aimed to evaluate the changes in the rumen fermentation and the structure and fibrolytic activities of rumen bacteria in camels fed barley straw and Egyptian clover hay. Materials and Methods Three fistulated camels were fed a diet containing barley straw for 30 days; then transitioned to a diet containing Egyptian clover hay for 30 days. In addition, bacterial media enriched with xylan and different cellulose sources, namely, filter paper, wheat straw, and alfalfa hay, were used to evaluate the ability of camel rumen bacteria to produce xylanase and cellulase enzymes. Results The camel group fed Egyptian clover hay showed higher crude protein intake, rumen ammonia, total volatile fatty acids, and acetic acid. Moreover, the camel group fed barley straw showed higher neutral detergent fiber intake, rumen pH, and propionic and butyric acids. Principal component analysis showed that bacterial communities were separated based on the forage type. Forage type affected the composition of rumen bacteria and most of the bacterial community was assigned to phylum Bacteroidetes and Firmicutes. Egyptian clover hay diet increased the proportions of genus Prevotella and Ruminococcus; while fed barley straw diet increased the Butyrivibrio, RC9_gut_group, and Fibrobacteres. The bacterial culture of the Egyptian clover hay fed group produced the greatest xylanase and the bacterial culture of the barley straw fed group produced the maximum cellulase. Conclusion Egyptian clover hay is recommended to feed camels in intensive production. Moreover, the bacterial community in the camel rumen is a promising source of lignocellulolytic enzymes.
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Affiliation(s)
- Alaa Emara Rabee
- Department of Animal and Poultry Nutrition, Desert Research Center, Cairo, Egypt
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9
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Abstract
The rumen ecosystem is a complex and dynamic environment, which hosts microorganisms including archaea, bacteria, protozoa, fungi, and viruses. These microorganisms interact with each other, altering the ruminal environment and substrates that will be available for the host digestion and metabolism. Viruses can infect the host and other microorganisms, which can drive changes in microorganisms' lysis rate, substrate availability, nutrient recycling, and population structure. The lysis of ruminal microorganisms' cells by viruses can release enzymes that enhance feedstuff fermentation, which may increase dietary nutrient utilization and feed efficiency. However, negative effects associated to viruses in the gastrointestinal tract have also been reported, in some cases, disrupting the dynamic stability of the ruminal microbiome, which can result in gastrointestinal dysfunctions. Therefore, the objective of this review is to summarize the current knowledge on ruminal virome, their interaction with other components of the microbiome and the effects on animal nutrition.
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Affiliation(s)
| | - Antonio P. Faciola
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
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10
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Khattab IM, Abdel-Wahed AM, Anele UY, Sallam SM, El-Zaiat HM. Comparative digestibility and rumen fermentation of camels and sheep fed different forage sources. Anim Biotechnol 2021:1-10. [PMID: 34689716 DOI: 10.1080/10495398.2021.1990939] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The present study evaluated the effects of forage sources on dry matter (DM) intake, digestibility, and fermentation parameters in camels vs. sheep. The study was arranged as a 2 × 3 factorial experiment in a completely randomized design by using two animal species (three ruminally cannulated female camels and three male sheep) and three forage sources. The forages were (1) alfalfa hay; 164 and 479 g/kg DM for crude protein (CP) and neutral detergent fiber (NDF), respectively, (2) berseem hay; 121 and 513 g/kg DM for CP and NDF, respectively, and (3) wheat straw (27.5 and 723 g/kg DM for CP and NDF, respectively). Higher DM intake [g/kg body weight (BW)] was noted in sheep compared to camel when alfalfa hay (p < 0.05) and berseem hay (p < 0.05) were fed but was similar between both species when they were fed wheat straw. Forage type rather than animal species had more effect on metabolic intake. Lower digestibility was noted in sheep with wheat straw (p < 0.05). Similar in situ degradability values for crude protein and DM were noted between camels and sheep. In situ degradability of NDF was higher (p < 0.05) in camel than sheep. Greater ruminal pH (p < 0.05) was noted in sheep vs. camels when berseem hay and wheat straw were fed. Lower ruminal passage rate (p < 0.05) was noted in camels and higher total mean retention time. It was concluded that sheep and camels had similar digestion capacities when fed berseem hay and alfalfa hay, however, camels are more efficient than sheep when fed wheat straw.
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Affiliation(s)
- Ibrahim M Khattab
- Department of Animal and Fish Production, Faculty of Desert and Environmental Agriculture, Matrouh University, Matrouh, Egypt
| | - Adel M Abdel-Wahed
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Egypt
| | - Uchenna Y Anele
- North Carolina Agricultural and Technical State University, Greensboro, North Carolina, USA
| | - Sobhy M Sallam
- Department of Animal Production, Faculty of Agriculture, University of Alexandria, Alexandria, Egypt
| | - Hani M El-Zaiat
- Department of Animal Production, Faculty of Agriculture, University of Alexandria, Alexandria, Egypt.,Department of Animal and Veterinary Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod, Oman
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11
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Rabee AE, Forster R, Sabra EA. Lignocelluloytic activities and composition of bacterial community in the camel rumen. AIMS Microbiol 2021; 7:354-367. [PMID: 34708177 PMCID: PMC8500796 DOI: 10.3934/microbiol.2021022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/15/2021] [Indexed: 11/29/2022] Open
Abstract
The camel is well-adapted to utilize the poor-quality forages in the harsh desert conditions as the camel rumen sustains fibrolytic microorganisms, mainly bacteria that are capable of breaking down the lignocellulosic biomass efficiently. Exploring the composition of the bacterial community in the rumen of the camel and quantifying their cellulolytic and xylanolytic activities could lead to understanding and improving fiber fermentation and discovering novel sources of cellulases and xylanases. In this study, Illumina MiSeq sequencing of the V4 region on 16S rRNA was applied to identify the bacterial and archaeal communities in the rumen of three camels fed wheat straw and broom corn. Furthermore, rumen samples were inoculated into bacterial media enriched with xylan and different cellulose sources, including filter paper (FP), wheat straw (WS), and alfalfa hay (AH) to assess the ability of rumen bacteria to produce endo-cellulase and endo-xylanase at different fermentation intervals. The results revealed that the phylum Bacteroidetes dominated the bacterial community and Candidatus Methanomethylophilus dominated the archaeal community. Also, most of the bacterial community has fibrolytic potential and the dominant bacterial genera were Prevotella, RC9_gut_group, Butyrivibrio, Ruminococcus, Fibrobacteres, and Treponema. The highest xylanase production (884.8 mU/mL) was observed at 7 days. The highest cellulase production (1049.5 mU/mL) was observed when rumen samples were incubated with Alfalfa hay for 7 days.
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Affiliation(s)
- Alaa Emara Rabee
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Egypt
| | - Robert Forster
- Lethbridge Research and Development Centre, Agriculture and Agrifood Canada, Lethbridge, AB, Canada
| | - Ebrahim A Sabra
- Animal Biotechnology Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
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12
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Rabee AE, Forster R, Elekwachi C, Sabra E, Lamara M. Comparative analysis of the metabolically active microbial communities in the rumen of dromedary camels under different feeding systems using total rRNA sequencing. PeerJ 2020; 8:e10184. [PMID: 33194403 PMCID: PMC7603790 DOI: 10.7717/peerj.10184] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/23/2020] [Indexed: 11/20/2022] Open
Abstract
Breakdown of plant biomass in rumen depends on interactions between bacteria, archaea, fungi, and protozoa; however, the majority of studies of the microbiome of ruminants, including the few studies of the rumen of camels, only studied one of these microbial groups. In this study, we applied total rRNA sequencing to identify active microbial communities in 22 solid and liquid rumen samples from 11 camels. These camels were reared at three stations that use different feeding systems: clover, hay and wheat straw (G1), fresh clover (G2), and wheat straw (G3). Bacteria dominated the libraries of sequence reads generated from all rumen samples, followed by protozoa, archaea, and fungi respectively. Firmicutes, Thermoplasmatales, Diplodinium, and Neocallimastix dominated bacterial, archaeal, protozoal and fungal communities, respectively in all samples. Libraries generated from camels reared at facility G2, where they were fed fresh clover, showed the highest alpha diversity. Principal co-ordinate analysis and linear discriminate analysis showed clusters associated with facility/feed and the relative abundance of microbes varied between liquid and solid fractions. This provides preliminary evidence that bacteria dominate the microbial communities of the camel rumen and these communities differ significantly between populations of domesticated camels.
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Affiliation(s)
- Alaa Emara Rabee
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Cairo, Egypt
| | - Robert Forster
- Lethbridge Research and Development Centre, Agriculture and Agrifood Canada, Lethbridge, AB, Canada
| | - Chijioke Elekwachi
- Lethbridge Research and Development Centre, Agriculture and Agrifood Canada, Lethbridge, AB, Canada
| | - Ebrahim Sabra
- Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Menoufia, Egypt
| | - Mebarek Lamara
- Institut de Recherche sur les Forêts, Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, QC, Canada
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13
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Guo W, Zhou M, Ma T, Bi S, Wang W, Zhang Y, Huang X, Guan LL, Long R. Survey of rumen microbiota of domestic grazing yak during different growth stages revealed novel maturation patterns of four key microbial groups and their dynamic interactions. Anim Microbiome 2020; 2:23. [PMID: 33499950 PMCID: PMC7807461 DOI: 10.1186/s42523-020-00042-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 06/30/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The development and maturation of rumen microbiota across the lifetime of grazing yaks remain unexplored due to the varied lifestyles and feed types of yaks as well as the challenges of obtaining samples. In addition, the interactions among four different rumen microbial groups (bacteria, archaea, fungi and protozoa) in the rumen of yak are not well defined. In this study, the rumen microbiota of full-grazing yaks aged 7 days to 12 years old was assessed to determine the maturation patterns of these four microbial groups and the dynamic interactions among them during different growth stages. RESULTS The rumen microbial groups (bacteria, archaea, protozoa and fungi) varied through the growth of yaks from neonatal (7 days) to adult (12 years), and the bacterial and archaeal groups were more sensitive to changes in growth stages compared to the two eukaryotic microbial groups. The age-discriminatory taxa within each microbial group were identified with the random forest model. Among them, Olsenella (bacteria), Group 10 sp., belonging to the family Methanomassiliicoccaceae (archaea), Orpinomyces (fungi), and Dasytricha (protozoa) contributed the most to discriminating the age of the rumen microbiota. Moreover, we found that the rumen archaea reached full maturation at 5 approximately years of age, and the other microbial groups matured between 5 and 8 years of age. The intra-interactions patterns and keystone species within each microbial group were identified by network analysis, and the inter-interactions among the four microbial groups changed with growth stage. Regarding the inter-interactions among the four microbial groups, taxa from bacteria and protozoa, including Christensenellaceae R-7 group, Prevotella 1, Trichostomatia, Ruminococcaceae UCG-014 and Lachnospiraceae, were the keystone species in the network based on betweenness centrality scores. CONCLUSIONS This study depicted a comprehensive view of rumen microbiota changes in different growth stages of grazing yaks. The results revealed the unique microbiota maturation trajectory and the intra- and inter-interactions among bacteria, archaea, fungi and protozoa in the rumen of grazing yaks across the lifetime of yaks. The information obtained in this study is vital for the future development of strategies to manipulate rumen microbiota in grazing yaks for better growth and performance in the harsh Qinghai-Tibetan Plateau ecosystem.
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Affiliation(s)
- Wei Guo
- College of Pastoral Agriculture Science and Technology, State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Lanzhou, 730020 China
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5 Canada
| | - Mi Zhou
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5 Canada
| | - Tao Ma
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5 Canada
- Key laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Sisi Bi
- School of Life Sciences, Lanzhou University, Lanzhou, 730020 China
| | - Weiwei Wang
- College of Pastoral Agriculture Science and Technology, State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Lanzhou, 730020 China
| | - Ying Zhang
- School of Public Health, Lanzhou University, Lanzhou, 730020 China
| | - Xiaodan Huang
- School of Public Health, Lanzhou University, Lanzhou, 730020 China
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5 Canada
| | - Ruijun Long
- College of Pastoral Agriculture Science and Technology, State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Lanzhou, 730020 China
- School of Life Sciences, Lanzhou University, Lanzhou, 730020 China
- International Centre for Tibetan Plateau Ecosystem Management, Lanzhou University, Lanzhou, 730020 China
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14
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Mishra P, Tulsani NJ, Jakhesara SJ, Dafale NA, Patil NV, Purohit HJ, Koringa PG, Joshi CG. Exploring the eukaryotic diversity in rumen of Indian camel (Camelus dromedarius) using 18S rRNA amplicon sequencing. Arch Microbiol 2020; 202:1861-1872. [PMID: 32448959 DOI: 10.1007/s00203-020-01897-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 04/13/2020] [Accepted: 05/11/2020] [Indexed: 12/18/2022]
Abstract
In addition to a wide variety of anaerobic and facultative anaerobic bacteria, camel rumen also harbors a diverse of eukaryotic organisms. In the present study, the eukaryotic communities of camel rumen were characterized using 18S rRNA amplicon sequencing. Metagenomic DNA was isolated from rumen samples of fourteen adult Bikaneri and Kachchhi breeds of camel fed different diets containing Jowar, Bajra, Maize, and Guar. Illumina sequencing generated 27,161,904 number of reads corresponding to 1543 total operational taxonomic units (OTUs). Taxonomic classification of community metagenome sequences from all the samples revealed the presence of 92 genera belonging to 16 different divisions, out of which Ciliophora (73%), Fungi (13%) and Streptophyta (9%) were found to be the most dominant. Notably, the abundance of Ciliophora was significantly higher in the case of Guar feed, while Fungi was significantly higher in the case of Maize feed, indicating the influence of cellulose and hemicellulose content of feedstuff on the composition of eukaryotes. The results suggest that the camel rumen eukaryotes are highly dynamic and depend on the type of diet given to the animal. Pearson's correlation analysis suggested the ciliate protozoa and fungi were negatively correlated with each other. To the best of our knowledge, this is first systematic study to characterize camel rumen eukaryotes, which has provided newer information regarding eukaryotic diversity patterns amongst camel fed on different diets.
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Affiliation(s)
- Priyaranjan Mishra
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Nilam J Tulsani
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India.
| | - Nishant A Dafale
- Environmental Genomic Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440020, India
| | - Niteen V Patil
- ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh, 334001, India
| | - Hemant J Purohit
- Environmental Genomic Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440020, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Center, MS Building, Block B & D, 6th Floor, GH Road, Sector-11, Gujarat, Gandhinagar, 382001, India
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15
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Characterization of Anaerobic Rumen Fungal Community Composition in Yak, Tibetan Sheep and Small Tail Han Sheep Grazing on the Qinghai-Tibetan Plateau. Animals (Basel) 2020; 10:ani10010144. [PMID: 31963125 PMCID: PMC7023293 DOI: 10.3390/ani10010144] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/06/2020] [Accepted: 01/14/2020] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Anaerobic rumen fungi play a vital role in fiber degradation. The objective of this study was to compare the anaerobic rumen fungal communities of full grazing ruminants in the Qinghai-Tibetan Plateau. Our results showed that the anaerobic rumen fungal community was affected by host species and the dynamic associations of them were host specific. This is the first study exploring the anaerobic rumen fungi in the full-grazing ruminants, which could lay a solid foundation to really identify fiber degradation fungal taxa using culture-dependent techniques in the future. Abstract The anaerobic rumen fungal community play a critical role in fibrous material degradation. However, there is a lack of data describing the composition of anaerobic rumen fungal community of full grazing ruminants in the Qinghai-Tibetan Plateau. For this reason, we employed the next-generation sequencing technique to elucidate the rumen fungal structure composition and evaluate the effects of host species on fungal communities. Community comparisons (Bray–Curtis index) between yak and Tibetan sheep revealed that the rumen fungal community was affected by host species (p < 0.05). The alpha diversity indices in the yak were significantly higher than in the Tibetan sheep and Small Tail Han sheep. Neocallimastigomycota was predominant regardless of host species. Within this phylum, unidentified genus of Neocallimastigaceae was the most dominant in all samples, followed by Piromyces and Orpinomyces. Moreover, the shared and unique OTUs in the rumen were identified and most of them belonged to the Orpinomyces. Co-occurrence network analysis identified that each animal species had their own keystone species and most of them were non-dominant flora. Our data indicate that host breeds override living environment as the key factor that determines fungal community in the rumen of grazing ruminants in the Qinghai-Tibetan Plateau.
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16
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Wang H, Li P, Liu X, Zhang C, Lu Q, Xi D, Yang R, Wang S, Bai W, Yang Z, Zhou R, Cheng X, Leng J. The Composition of Fungal Communities in the Rumen of Gayals ( Bos frontalis), Yaks ( Bos grunniens), and Yunnan and Tibetan Yellow Cattle ( Bos taurs). Pol J Microbiol 2019; 68:505-514. [PMID: 31880894 PMCID: PMC7260705 DOI: 10.33073/pjm-2019-050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 11/14/2022] Open
Abstract
The rumen is a microbial-rich ecosystem in which rumen fungi play an important role in the feed digestion of ruminants. The composition of rumen fungi in free-range ruminants such as gayals, yaks, Tibetan yellow cattle, and the domesticated Yunnan yellow cattle was investigated by sequencing an internal transcribed spacer region 1 (ITS1) using Illumina MiSeq. A total of 285 092 optimized sequences and 904 operational taxonomic units (OTUs) were obtained from the four cattle breeds. The rumen fungi abundance and Chao and Simpson indexes were all higher in free-range ruminants than in domesticated ruminants. Three fungal phyla were identified by sequence comparison: Neocallimastigomycota, Basidiomycota, and Ascomycota. Basidiomycota and Ascomycota have very low abundance in the rumen of four breeds cattle but anaerobic fungi (AF) Neocallimastigomycota occurred in a high abundance. In Neocallimastigomycota, the dominant genera were Piromyces, Anaeromyces, Cyllamyces, Neocallimastix, and Orpionmyces in four cattle breeds. The composition of the major genera of Neocallimastigaceae varied greatly among the four cattle breeds. The unclassified genera were unequally distributed in gayals, yaks, Tibetan and Yunnan yellow cattle, accounting for 90.63%, 98.52%, 97.79%, and 27.01% respectively. It appears that free-range ruminants have more unknown rumen fungi than domesticated ruminants and the cattle breeds and animal diets had an impact on the diversity of rumen fungi.
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Affiliation(s)
- Houfu Wang
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China
| | - Pengfei Li
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China
| | - Xuchuan Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Chunyong Zhang
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China ; Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Qiongfen Lu
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China ; Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Renhui Yang
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China
| | - Shuling Wang
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China
| | - Wenshun Bai
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Zhen Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Rongkang Zhou
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Xiao Cheng
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Jing Leng
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China ; Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
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17
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Rabee AE, Forster RJ, Elekwachi CO, Kewan KZ, Sabra E, Mahrous HA, Khamiss OA, Shawket SM. Composition of bacterial and archaeal communities in the rumen of dromedary camel using cDNA-amplicon sequencing. Int Microbiol 2019; 23:137-148. [PMID: 31432356 DOI: 10.1007/s10123-019-00093-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 06/30/2019] [Accepted: 07/21/2019] [Indexed: 11/25/2022]
Abstract
The camel is known to survive in harsh environmental conditions, due to its higher digestive efficiency of high-fiber diets compared with other ruminants. However, limited data are available on the microbial community in the rumen of a camel. In this study, the Illumina sequencing of V4 region of 16S rRNA genes based on RNA isolation was employed to get insight into the bacterial and archaeal communities associated with liquid and solid rumen fractions in eight camels under different feeding systems. Camels in group C1 were fed Egyptian clover hay plus concentrates mixture and camels of group C2 were fed fresh Egyptian clover. The results showed that liquid fraction has higher operational taxonomic units (OTUs) than solid fraction, and camel group C1 showed a higher microbial diversity than C2. The UniFrac analysis indicated that the microbial communities in camel groups are distinct. Moreover, phylum Firmicutes and Bacteroidetes dominated the bacterial community and Candidatus Methanomethylophilus dominated the archaeal community with a significant difference in the relative abundance between camel groups. Dominant bacterial genera were Prevotella, Fibrobacteres, Ruminococcus, and Butyrivibrio. There were many negative and positive correlations between and within bacterial and archaeal genera. The composition of microbial community in the rumen of a camel is similar to other ruminants with differences in the abundance.
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Affiliation(s)
- Alaa E Rabee
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Egypt.
| | | | | | - Khaled Z Kewan
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Egypt
| | - Ebrahim Sabra
- Genetic Engineering and Biotechnology Research Institute, Sadat City University, Sadat City, Egypt
| | - Hoda A Mahrous
- Genetic Engineering and Biotechnology Research Institute, Sadat City University, Sadat City, Egypt
| | - Omaima A Khamiss
- Genetic Engineering and Biotechnology Research Institute, Sadat City University, Sadat City, Egypt
| | - Safinaze M Shawket
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Egypt
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18
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Hitch TCA, Edwards JE, Gilbert RA. Metatranscriptomics reveals mycoviral populations in the ovine rumen. FEMS Microbiol Lett 2019; 366:5533320. [DOI: 10.1093/femsle/fnz161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/16/2019] [Indexed: 12/26/2022] Open
Abstract
ABSTRACT
The rumen is known to contain DNA-based viruses, although it is not known whether RNA-based viruses that infect fungi (mycoviruses) are also present. Analysis of publicly available rumen metatranscriptome sequence data from sheep rumen samples (n = 20) was used to assess whether RNA-based viruses exist within the ovine rumen. A total of 2466 unique RNA viral contigs were identified that had homology to nine viral families. The Partitiviridae was the most consistently observed mycoviral family. High variation in the abundance of each detected mycovirus suggests that rumen mycoviral populations vary greatly between individual sheep. Functional analysis of the genes within the assembled mycoviral contigs suggests that the mycoviruses detected had simple genomes, often only carrying the machinery required for replication. The fungal population of the ovine rumen was also assessed using metagenomics data from the same samples, and was consistently dominated by the phyla Ascomycota and Basidomycota. The strictly anaerobic phyla Neocallimastigomycota were also present in all samples but at a low abundance. This preliminary investigation has provided clear evidence that mycoviruses with RNA genomes exist in the rumen, with further in-depth studies now required to characterise this mycoviral community and determine its role in the rumen.
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Affiliation(s)
- Thomas C A Hitch
- Institute of Biological, Environmental and Rural Sciences, Penglais Campus, Aberystwyth University, Aberystwyth, UK
- Institute of Medical Microbiology, RWTH Aachen University Hospital, Aachen, Germany
| | - Joan E Edwards
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Rosalind A Gilbert
- Department of Agriculture and Fisheries, Brisbane, Australia
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
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