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Teng Z, Liu S, Zhang L, Zhang L, Liu S, Fu T, Zhang N, Gao T. Tea Polyphenols Inhibit Methanogenesis and Improve Rumen Epithelial Transport in Dairy Cows. Animals (Basel) 2024; 14:2569. [PMID: 39272354 PMCID: PMC11394105 DOI: 10.3390/ani14172569] [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: 08/07/2024] [Revised: 08/28/2024] [Accepted: 09/02/2024] [Indexed: 09/15/2024] Open
Abstract
This study systematically investigated the effects of tea polyphenols on methane (CH4) production and the rumen epithelial cell transport capability in cattle using both in vitro and animal experiments, employing multi-omics techniques. The in vitro results demonstrated that, compared to the control group, tea polyphenols significantly reduced CH4 production and the acetate/propionate ratio (p < 0.05). Tea polyphenols reduced CH4 production by inhibiting the relative abundance of unclassified_d_Archaea methanogens and the protozoa Pseudoentodinium and g__Balantioides. The animal experiments showed that tea polyphenols significantly increased the concentrations of T-AOC and GSH-PX in bovine blood (p < 0.05). In addition, microbial groups such as Rikenellaceae_RC9_gut_group, Ruminococcaceae_NK4A214_group, and Butyrivibrio_2 were significantly enriched in the ruminal fluid of the tea polyphenol group (p < 0.05). The proteomic results indicated significant upregulation of proteins such as COIII, S100A8, FABP1, SLC2A8, and SLC29A1 (p < 0.05) and downregulation of proteins including HBB, RAB4A, RBP4, LOC107131172, HBA, and ZFYVE19 (p < 0.05), with FABP1 showing a positive correlation with propionate concentration, and RAB4A had a negative correlation (p < 0.05). Overall, tea polyphenols modulate the microbial composition within the rumen, inhibiting CH4 production and enhancing the host's rumen epithelial cell transport capacity for volatile fatty acids.
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Affiliation(s)
- Zhanwei Teng
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Postdoctoral Research Base, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Shuai Liu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Lijie Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Liyang Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Shenhe Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Tong Fu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Ningning Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Tengyun Gao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
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2
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Han B, Zhou W, Chen R, Tian S, Gong H, Wang Y, Xu Q, Bian M. Multi-factor analysis of the quality of cellar mud of Luzhou-flavor liquor in Yibin production area. Food Sci Nutr 2024; 12:5231-5249. [PMID: 39055204 PMCID: PMC11266919 DOI: 10.1002/fsn3.4174] [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: 01/05/2024] [Revised: 03/14/2024] [Accepted: 04/08/2024] [Indexed: 07/27/2024] Open
Abstract
The aim of this study was to conduct a thorough scientific investigation into the similarities and differences in the quality of the cellars of different Luzhou-flavor liquor wineries in Yibin production area and the reasons for them. This study analyzed cellar mud samples from five wineries in Yibin production area. The analysis of volatile flavor compounds was carried out using headspace solid-phase microextraction and gas chromatography-mass spectrometry. The bacterial and archaeal community structures and their correlations were analyzed by high-throughput sequencing. The study indicates that the Distillery A had the highest levels of ammonium nitrogen and effective phosphorus, Distillery F had the highest humus levels, and Distillery I had the highest pH levels. The community structure of the principal bacterial and archaeal communities in the five subterranean clays exhibited similarity, and all samples were dominated by Firmicutes as the primary bacterial group. However, there was variation in bacterial abundance. The cellar mud also has obvious regional differences, and there are three genera of differentially dominant archaea in the archaea. In summary, significant differences were observed in the physicochemical indexes of bacterial and archaeal abundance across all five samples. These differences led to variations in both the content and composition of volatile constituents.
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Affiliation(s)
- Baolin Han
- Sichuan University of Science & EngineeringYibinChina
| | - Weitao Zhou
- Sichuan University of Science & EngineeringYibinChina
| | - Rangfang Chen
- Sichuan University of Science & EngineeringYibinChina
| | - Shulin Tian
- Sichuan University of Science & EngineeringYibinChina
| | - Hucheng Gong
- Sichuan University of Science & EngineeringYibinChina
| | - Yu Wang
- Sichuan University of Science & EngineeringYibinChina
| | - Qiang Xu
- Sichuan University of Science & EngineeringYibinChina
| | - Minghong Bian
- Sichuan University of Science & EngineeringYibinChina
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3
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Lourenco JM, Callaway TR. Editorial: Impact of Special Issue "The Microbial Population of the Gastrointestinal Tract of Animals: Impacts on Host Physiology". Microorganisms 2024; 12:859. [PMID: 38792689 PMCID: PMC11124161 DOI: 10.3390/microorganisms12050859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/12/2024] [Indexed: 05/26/2024] Open
Abstract
In recent years, there has been an exponential increase in the number of papers that have investigated the microbiome of animals and humans [...].
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Affiliation(s)
| | - Todd R. Callaway
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA;
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4
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Anstett J, Plominsky AM, DeLong EF, Kiesser A, Jürgens K, Morgan-Lang C, Stepanauskas R, Stewart FJ, Ulloa O, Woyke T, Malmstrom R, Hallam SJ. A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters. Sci Data 2023; 10:332. [PMID: 37244914 DOI: 10.1038/s41597-023-02222-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 05/10/2023] [Indexed: 05/29/2023] Open
Abstract
Oxygen-deficient marine waters referred to as oxygen minimum zones (OMZs) or anoxic marine zones (AMZs) are common oceanographic features. They host both cosmopolitan and endemic microorganisms adapted to low oxygen conditions. Microbial metabolic interactions within OMZs and AMZs drive coupled biogeochemical cycles resulting in nitrogen loss and climate active trace gas production and consumption. Global warming is causing oxygen-deficient waters to expand and intensify. Therefore, studies focused on microbial communities inhabiting oxygen-deficient regions are necessary to both monitor and model the impacts of climate change on marine ecosystem functions and services. Here we present a compendium of 5,129 single-cell amplified genomes (SAGs) from marine environments encompassing representative OMZ and AMZ geochemical profiles. Of these, 3,570 SAGs have been sequenced to different levels of completion, providing a strain-resolved perspective on the genomic content and potential metabolic interactions within OMZ and AMZ microbiomes. Hierarchical clustering confirmed that samples from similar oxygen concentrations and geographic regions also had analogous taxonomic compositions, providing a coherent framework for comparative community analysis.
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Affiliation(s)
- Julia Anstett
- Graduate Program in Genome Sciences and Technology, Genome Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Alvaro M Plominsky
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI, 96822, USA
| | - Alyse Kiesser
- School of Engineering, The University of British Columbia, Kelowna, BC, Canada
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research, Warnemünde, Germany
| | - Connor Morgan-Lang
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | | | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Osvaldo Ulloa
- Departamento de Oceanografía, Universidad de Concepción, Casilla 160-C, 4070386, Concepción, Chile
- Instituto Milenio de Oceanografía, Casilla 1313, 4070386, Concepción, Chile
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rex Malmstrom
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven J Hallam
- Graduate Program in Genome Sciences and Technology, Genome Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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5
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Takizawa S, Shinkai T, Saito K, Fukumoto N, Arai Y, Hirai T, Maruyama M, Takeda M. Effect of rumen microbiota transfaunation on the growth, rumen fermentation, and microbial community of early separated Japanese Black cattle. Anim Sci J 2023; 94:e13876. [PMID: 37818871 DOI: 10.1111/asj.13876] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/20/2023] [Accepted: 09/07/2023] [Indexed: 10/13/2023]
Abstract
This study aimed to investigate the effect of rumen microbiota transfaunation on the growth, rumen fermentation, and the microbial community of Japanese Black cattle that were separated early from their dams. Here, 24 calves were separated from their dams immediately after calving, 12 of which were transfaunated via inoculation with rumen fluid from adult cattle at the age of 2 months while the remaining 12 were kept unfaunated (not-inoculated). Feed efficiency monitoring was performed during 7-10 months of age. Body weight and feed intake were not significantly different between the transfaunated and unfaunated cattle. Transfaunation increased the relative levels of acetate and butyrate but decreased those of propionate, which increased the non-glucogenic/glucogenic short-chain fatty acid ratio. Microbial 16S, 18S, and ITS ribosomal RNA gene amplicon analysis showed that rumen microbial diversity and composition differed between transfaunated and unfaunated cattle; transfaunation increased the abundance of acetate- and butyrate-producing bacteria, and decreased the abundance of bacterial genera associated with propionate production. Transfaunation also increased the abundance of Methanomassiliicoccaceae_group10 (1.94% vs. 0.05%) and Neocallimastix (27.1% vs. 6.8%) but decreased that of Methanomicrobium (<0.01% vs. 0.06%). Our findings indicate that rumen microbiota transfaunation shifts rumen fermentation toward acetate and butyrate production through a change in the rumen microbial composition in Japanese Black cattle.
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Affiliation(s)
- Shuhei Takizawa
- National Agriculture and Food Research Organization, Institute of Livestock and Grassland Science, Tsukuba, Japan
| | - Takumi Shinkai
- National Agriculture and Food Research Organization, Institute of Livestock and Grassland Science, Tsukuba, Japan
| | - Kunihiko Saito
- National Livestock Breeding Center Tokachi Station, Otofuke, Japan
| | - Natsuko Fukumoto
- National Livestock Breeding Center Tokachi Station, Otofuke, Japan
| | - Yukari Arai
- National Livestock Breeding Center Tokachi Station, Otofuke, Japan
- Ministry of Agriculture, Forestry and Fisheries, Tokyo, Japan
| | - Tomokazu Hirai
- National Livestock Breeding Center Tokachi Station, Otofuke, Japan
| | | | - Masayuki Takeda
- National Livestock Breeding Center Tokachi Station, Otofuke, Japan
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6
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Inabu Y, Taguchi Y, Miyamoto H, Etoh T, Shiotsuka Y, Fujino R, Okada T, Udagawa M, Tsuji N, Matsuura M, Tsuboi A, Kato T, Kodama H, Ohno H, Takahashi H. Development of a novel feeding method for Japanese black calves with thermophile probiotics at postweaning. J Appl Microbiol 2022; 132:3870-3882. [PMID: 35261112 DOI: 10.1111/jam.15519] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 02/23/2022] [Accepted: 03/03/2022] [Indexed: 11/29/2022]
Abstract
AIMS Probiotic effects of compost containing thermophiles on productivity have been reported in domestic animals, although not cattle. We evaluated the effects of administering Caldibacillus hisashii, a thermophile contained in compost, on growth, blood components, faecal organic acid concentrations and microbiota population in Japanese black calves. METHODS AND RESULTS Calves were administered C. hisashii from 3 to 5 mo of age. Administering C. hisashii decreased feed intake without affecting body weight, indicating that feed efficiency is improved by administration. Administering C. hisashii decreased plasma insulin concentration without affecting glucose and nonesterified fatty acid concentrations. Chao1 was decreased by exposure at 5 mo of age. Similarly, weighted- and unweighted UniFrac distances were affected by treatment at 5 mo of age. Faecal abundance of the phylum Bacteroidetes tended to be increased by exposure. Faecal propionic acid concentration was correlated positively with faecal abundance of phylum Bacteroidetes but negatively with that of Firmicutes. Interestingly, the population of the genus Methanobrevibacter, representing the majority of methanogens, was lowered by exposure and was negatively correlated with faecal propionic acid concentration. CONCLUSION Administration of C. hisashii has the potential to improve growth performance of Japanese black calves and to contribute to reducing environmental load, which may be associated with altered endocrine kinetics and gut microbial populations. SIGNIFICANCE AND IMPACTS OF THE STUDY This study revealed that isolated thermophiles included in compost may exert probiotic effects on calves.
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Affiliation(s)
- Yudai Inabu
- Kuju Agricultural Research Center, Graduate School of Agriculture, Kyushu University, Oita, Japan
| | - Yutaka Taguchi
- Kuju Agricultural Research Center, Graduate School of Agriculture, Kyushu University, Oita, Japan
| | - Hirokuni Miyamoto
- Graduate School of Horticulture, Chiba University, Chiba, Japan.,RIKEN IMS, Yokohama, Kanagawa, Japan.,Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Japan.,Sermas, Co., Ltd., Chiba, Japan
| | - Tetsuji Etoh
- Kuju Agricultural Research Center, Graduate School of Agriculture, Kyushu University, Oita, Japan
| | - Yuji Shiotsuka
- Kuju Agricultural Research Center, Graduate School of Agriculture, Kyushu University, Oita, Japan
| | - Ryoichi Fujino
- Kuju Agricultural Research Center, Graduate School of Agriculture, Kyushu University, Oita, Japan
| | - Toru Okada
- Asuka Animal Health Co., Ltd., Tokyo, Japan
| | | | | | - Makiko Matsuura
- Graduate School of Horticulture, Chiba University, Chiba, Japan.,Sermas, Co., Ltd., Chiba, Japan
| | - Arisa Tsuboi
- Graduate School of Horticulture, Chiba University, Chiba, Japan.,Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Japan.,Sermas, Co., Ltd., Chiba, Japan.,RIKEN CSRS, Yokohama, Kanagawa, Japan
| | | | - Hiroaki Kodama
- Graduate School of Horticulture, Chiba University, Chiba, Japan
| | | | - Hideyuki Takahashi
- Kuju Agricultural Research Center, Graduate School of Agriculture, Kyushu University, Oita, Japan
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7
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Changed Rumen Fermentation, Blood Parameters, and Microbial Population in Fattening Steers Receiving a High Concentrate Diet with Saccharomyces cerevisiae Improve Growth Performance. Vet Sci 2021; 8:vetsci8120294. [PMID: 34941821 PMCID: PMC8707694 DOI: 10.3390/vetsci8120294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/23/2021] [Accepted: 11/26/2021] [Indexed: 11/18/2022] Open
Abstract
The effect of dry yeast (DY) (Saccharomyces cerevisiae) supplementation in a high-concentrate diet was evaluated for rumen fermentation, blood parameters, microbial populations, and growth performance in fattening steers. Sixteen crossbred steers (Charolais x American Brahman) at 375 ± 25 kg live weight were divided into four groups that received DY supplementation at 0, 5, 10, and 15 g/hd/d using a completely randomized block design. Basal diets were fed as a total mixed ration (roughage to concentrate ratio of 30:70). Results showed that supplementation with DY improved dry matter (DM) intake and digestibility of organic matter (OM), neutral detergent fiber (NDF), and acid detergent fiber (ADF) (p < 0.05), but DM and crude protein (CP) were similar among treatments (p > 0.05). Ruminal pH (>6.0) of fattening steer remained stable (p > 0.05), and pH was maintained at or above 6.0 with DY. The concentration of propionic acid (C3) increased (p < 0.05) with 10 and 15 g/hd/d DY supplementation, while acetic acid (C2) and butyric acid (C4) decreased. Methane (CH4) production in the rumen decreased as DY increased (p < 0.05). Fibrobacter succinogenes and Ruminococcus flavefaciens populations increased (p < 0.05), whereas protozoal and methanogen populations decreased with DY addition at 10 and 15 g/hd/d, while Ruminococcus albus did not change (p > 0.05) among the treatments. Adding DY at 10 and 15 g/hd/d improved growth performance. Thus, the addition of DY to fattening steers with a high concentrate diet improved feed intake, nutrient digestibility, rumen ecology, and growth performance, while mitigating ruminal methane production.
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8
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Wang M, Chen M, Bai J, Zhang J, Su R, Franco M, Ding Z, Zhang X, Zhang Y, Guo X. Ensiling characteristics, in vitro rumen fermentation profile, methane emission and archaeal and protozoal community of silage prepared with alfalfa, sainfoin and their mixture. Anim Feed Sci Technol 2021. [DOI: 10.1016/j.anifeedsci.2021.115154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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9
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Duan Y, Lian J, Wang L, Wang X, Luo Y, Wang W, Wu F, Zhao J, Ding Y, Ma J, Li Y, Li Y. Variation in Soil Microbial Communities Along an Elevational Gradient in Alpine Meadows of the Qilian Mountains, China. Front Microbiol 2021; 12:684386. [PMID: 34248904 PMCID: PMC8270674 DOI: 10.3389/fmicb.2021.684386] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/24/2021] [Indexed: 01/22/2023] Open
Abstract
Bacterial, archaeal, and eukaryota diversity in mountainous areas varies along elevational gradients, but details remain unclear. Here, we use a next-generation sequencing method based on 16S/18S rRNA to reveal the soil microbial diversity and community compositions of alpine meadow ecosystems along an elevation span of nearly 2,000 m (1,936-3,896 m) in China's Qilian Mountains. Both bacterial and eukaryota diversity increased linearly with increasing elevation, whereas archaeal diversity increased, but not significantly. The diversity patterns of several phyla in the bacterial, archaeal, and eukaryota communities were consistent with the overall elevational trend, but some phyla did not follow this pattern. The soil microbial community compositions were shaped by the coupled effects of regional climate and local soil properties. Intradomain links were more important than interdomain links in the microbial network of the alpine meadows, and these links were mostly positive. The bacteria formed more connections than either archaea or eukaryota, but archaea may be more important than bacteria in building the soil microbial co-occurrence network in this region. Our results provide new visions on the formation and maintenance of soil microbial diversity along an elevational gradient and have implications for microbial responses to climate change in alpine ecosystems.
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Affiliation(s)
- Yulong Duan
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, China
| | - Jie Lian
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, China
| | - Lilong Wang
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, China
| | - Xuyang Wang
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, China
| | - Yongqing Luo
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, China
| | - Wanfu Wang
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Dunhuang Academy, Dunhuang, China.,MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Fasi Wu
- National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Dunhuang Academy, Dunhuang, China.,MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jianhua Zhao
- Shanghai Majorbio Bio-Pharm Technology Co., Ltd., Shanghai, China
| | - Yun Ding
- Shanghai Majorbio Bio-Pharm Technology Co., Ltd., Shanghai, China
| | - Jun Ma
- Gansu Qilian Mountains National Nature Reserve Authority, Zhangye, China
| | - Yulin Li
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuqiang Li
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, China.,University of Chinese Academy of Sciences, Beijing, China
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10
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Lai D, Hedlund BP, Xie W, Liu J, Phelps TJ, Zhang C, Wang P. Impact of Terrestrial Input on Deep-Sea Benthic Archaeal Community Structure in South China Sea Sediments. Front Microbiol 2020; 11:572017. [PMID: 33224115 PMCID: PMC7674655 DOI: 10.3389/fmicb.2020.572017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022] Open
Abstract
Archaea are widespread in marine sediments and play important roles in the cycling of sedimentary organic carbon. However, factors controlling the distribution of archaea in marine sediments are not well understood. Here we investigated benthic archaeal communities over glacial-interglacial cycles in the northern South China Sea and evaluated their responses to sediment organic matter sources and inter-species interactions. Archaea in sediments deposited during the interglacial period Marine Isotope Stage (MIS) 1 (Holocene) were significantly different from those in sediments deposited in MIS 2 and MIS 3 of the Last Glacial Period when terrestrial input to the South China Sea was enhanced based on analysis of the long-chain n-alkane C31. The absolute archaeal 16S rRNA gene abundance in subsurface sediments was highest in MIS 2, coincident with high sedimentation rates and high concentrations of total organic carbon. Soil Crenarchaeotic Group (SCG; Nitrososphaerales) species, the most abundant ammonia-oxidizing archaea in soils, increased dramatically during MIS 2, likely reflecting transport of terrestrial archaea during glacial periods with high sedimentation rates. Co-occurrence network analyses indicated significant association of SCG archaea with benthic deep-sea microbes such as Bathyarchaeota and Thermoprofundales in MIS 2 and MIS 3, suggesting potential interactions among these archaeal groups. Meanwhile, Thermoprofundales abundance was positively correlated with total organic carbon (TOC), along with n-alkane C31 and sedimentation rate, indicating that Thermoprofundales may be particularly important in processing of organic carbon in deep-sea sediments. Collectively, these results demonstrate that the composition of heterotrophic benthic archaea in the South China Sea may be influenced by terrestrial organic input in tune with glacial-interglacial cycles, suggesting a plausible link between global climate change and microbial population dynamics in deep-sea marine sediments.
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Affiliation(s)
- Dengxun Lai
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China.,School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States.,Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, United States
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Jingjing Liu
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Tommy J Phelps
- Earth and Planetary Sciences, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Shanghai Sheshan National Geophysical Observatory, Shanghai, China
| | - Peng Wang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
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11
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Tan C, Ramírez-Restrepo CA, Shah AM, Hu R, Bell M, Wang Z, McSweeney C. The community structure and microbial linkage of rumen protozoa and methanogens in response to the addition of tea seed saponins in the diet of beef cattle. J Anim Sci Biotechnol 2020; 11:80. [PMID: 32832076 PMCID: PMC7422560 DOI: 10.1186/s40104-020-00491-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 06/25/2020] [Indexed: 12/17/2022] Open
Abstract
Background This study investigated changes in rumen protozoal and methanogenic communities, along with the correlations among microbial taxa and methane (CH4) production of six Belmont Red Composite beef steers fed tea seed saponins (TSS). Animals were fed in three consecutive feeding periods, a high-grain basal diet for 14 d (BD period) then a period of progressive addition of TSS to the basal diet up to 30 g/d for 20 d (TSS period), followed by the basal diet for 13 d without TSS (BDP post-control period). Results The study found that TSS supplementation decreased the amount of the protozoal genus Entodinium and increased Polyplastron and Eudiplodinium genera. During BDP period, the protozoa community of steers did not return to the protozoal profiles observed in BD period, with higher proportions of Metadinium and Eudiplodinium and lower Isotricha. The addition of TSS was found to change the structure of methanogen community at the sub-genus level by decreasing the abundance of methanogens in the SGMT clade and increasing the abundance of methanogens in the RO clade. The correlation analysis indicated that the abundance of SGMT clade methanogens were positively correlated with Isotricha, and Isotricha genus and SGMT clade methanogens were positively correlated with CH4 production. While RO clade were positively correlated with the proportion of Metadinium genus, which was negatively correlated with CH4 emission. Conclusions These results suggest that different genera of rumen protozoa ciliates appear to be selectively inhibited by TSS, and the change in methanogen community at the subgenus level may be due to the mutualistic relationships between methanogens and rumen ciliates.
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Affiliation(s)
- Cui Tan
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Carlos A Ramírez-Restrepo
- Commonwealth Scientific and Industrial Research Organisation, CSIRO Agriculture and Food, Australian Tropical Sciences and Innovation Precinct, James Cook University, Townsville, QLD 4811 Australia.,Present address: CR Eco-efficient Agriculture Consultancy (CREAC), 46 Bilbao Place, Bushland Beach, QLD 4818 Australia
| | - Ali Mujtaba Shah
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, 611130 Sichuan China.,Department of Livestock Production, Shaheed Benazir Bhutto University of Veterinary and Animal Sciences, Sakrand, Sindh 67210 Pakistan
| | - Rui Hu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, 611130 Sichuan China.,"Low Carbon Breeding Cattle and Safety Production", University Key Laboratory of Sichuan Province, Ya'an, 625014 Sichuan China
| | - Matt Bell
- School of Biosciences, University of Nottingham, Sutton Bonington, Loughborough, LE12 5RD UK
| | - Zhisheng Wang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, 611130 Sichuan China.,"Low Carbon Breeding Cattle and Safety Production", University Key Laboratory of Sichuan Province, Ya'an, 625014 Sichuan China
| | - Chris McSweeney
- CSIRO Agriculture, Queensland BioScience Precinct, St Lucia, Brisbane, QLD 4067 Australia
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12
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Hirakata Y, Hatamoto M, Oshiki M, Watari T, Araki N, Yamaguchi T. Food selectivity of anaerobic protists and direct evidence for methane production using carbon from prey bacteria by endosymbiotic methanogen. ISME JOURNAL 2020; 14:1873-1885. [PMID: 32341474 DOI: 10.1038/s41396-020-0660-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 01/28/2023]
Abstract
Anaerobic protists are major predators of prokaryotes in anaerobic ecosystems. However, little is known about the predation behavior of anaerobic protists because almost none have been cultured. In particular, these characteristics of anaerobic protists in the phyla Metamonada and Cercozoa have not been reported previously. In this study, we isolated three anaerobic protists, Cyclidium sp., Trichomitus sp., and Paracercomonas sp., from anaerobic granular sludge in an up-flow anaerobic sludge blanket reactor used to treat domestic sewage. Ingestion and digestion of food bacteria by anaerobic protists with or without endosymbiotic methanogens were demonstrated using tracer experiments with green fluorescent protein and a stable carbon isotope. These tracer experiments also demonstrated that Cyclidium sp. supplied CO2 and hydrogen to endosymbiotic methanogens. While Cyclidium sp. and Trichomitus sp. ingested both Gram-negative and -positive bacteria, Paracercomonas sp. could only take up Gram-negative bacteria. Archaeal cells such as Methanobacterium beijingense and Methanospirillum hungatei did not support the growth of these protists. Metabolite patterns of all three protists differed and were influenced by food bacterial species. These reported growth rates, ingestion rates, food selectivity, and metabolite patterns provide important insights into the ecological roles of these protists in anaerobic ecosystems.
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Affiliation(s)
- Yuga Hirakata
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Masashi Hatamoto
- Department of Civil and Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan.
| | - Mamoru Oshiki
- Department of Civil Engineering, Nagaoka College, National Institute of Technology, Nagaoka, Niigata, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Nobuo Araki
- Department of Civil Engineering, Nagaoka College, National Institute of Technology, Nagaoka, Niigata, Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Niigata, Japan.,Department of Civil and Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
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13
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Li M, Mi T, Yu Z, Ma M, Zhen Y. Planktonic Bacterial and Archaeal Communities in an Artificially Irrigated Estuarine Wetland: Diversity, Distribution, and Responses to Environmental Parameters. Microorganisms 2020; 8:microorganisms8020198. [PMID: 32023944 PMCID: PMC7074933 DOI: 10.3390/microorganisms8020198] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 11/21/2022] Open
Abstract
Bacterial and archaeal communities play important roles in wetland ecosystems. Although the microbial communities in the soils and sediments of wetlands have been studied extensively, the comprehensive distributions of planktonic bacterial and archaeal communities and their responses to environmental variables in wetlands remain poorly understood. The present study investigated the spatiotemporal characteristics of the bacterial and archaeal communities in the water of an artificially irrigated estuarine wetland of the Liaohe River, China, explored whether the wetland effluent changed the bacterial and archaeal communities in the Liaohe River, and evaluated the driving environmental factors. Within the study, 16S rRNA quantitative PCR methods and MiSeq high-throughput sequencing were used. The bacterial and archaeal 16S rRNA gene abundances showed significant temporal variation. Meanwhile, the bacterial and archaeal structures showed temporal but not spatial variation in the wetland and did not change in the Liaohe River after wetland drainage. Moreover, the bacterial communities tended to have higher diversity in the wetland water in summer and in the scarce zone, while a relatively higher diversity of archaeal communities was found in autumn and in the intensive zone. DO, pH and PO4-P were proven to be the essential environmental parameters shaping the planktonic bacterial and archaeal community structures in the Liaohe River estuarine wetland (LEW). The LEW had a high potential for methanogenesis, which could be reflected by the composition of the microbial communities.
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Affiliation(s)
- Mingyue Li
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Tiezhu Mi
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Zhigang Yu
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education/Institute for Advanced Ocean Study, Ocean University of China, Qingdao 266100, China
| | - Manman Ma
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Yu Zhen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
- Correspondence: ; Tel.: +86-532-6678-1940
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14
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Muñoz-Tamayo R, Popova M, Tillier M, Morgavi DP, Morel JP, Fonty G, Morel-Desrosiers N. Hydrogenotrophic methanogens of the mammalian gut: Functionally similar, thermodynamically different-A modelling approach. PLoS One 2019; 14:e0226243. [PMID: 31826000 PMCID: PMC6905546 DOI: 10.1371/journal.pone.0226243] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/24/2019] [Indexed: 12/11/2022] Open
Abstract
Methanogenic archaea occupy a functionally important niche in the gut microbial ecosystem of mammals. Our purpose was to quantitatively characterize the dynamics of methanogenesis by integrating microbiology, thermodynamics and mathematical modelling. For that, in vitro growth experiments were performed with pure cultures of key methanogens from the human and ruminant gut, namely Methanobrevibacter smithii, Methanobrevibacter ruminantium and Methanobacterium formicium. Microcalorimetric experiments were performed to quantify the methanogenesis heat flux. We constructed an energetic-based mathematical model of methanogenesis. Our model captured efficiently the dynamics of methanogenesis with average concordance correlation coefficients of 0.95 for CO2, 0.98 for H2 and 0.97 for CH4. Together, experimental data and model enabled us to quantify metabolism kinetics and energetic patterns that were specific and distinct for each species despite their use of analogous methane-producing pathways. Then, we tested in silico the interactions between these methanogens under an in vivo simulation scenario using a theoretical modelling exercise. In silico simulations suggest that the classical competitive exclusion principle is inapplicable to gut ecosystems and that kinetic information alone cannot explain gut ecological aspects such as microbial coexistence. We suggest that ecological models of gut ecosystems require the integration of microbial kinetics with nonlinear behaviours related to spatial and temporal variations taking place in mammalian guts. Our work provides novel information on the thermodynamics and dynamics of methanogens. This understanding will be useful to construct new gut models with enhanced prediction capabilities and could have practical applications for promoting gut health in mammals and mitigating ruminant methane emissions.
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Affiliation(s)
- Rafael Muñoz-Tamayo
- UMR Modélisation Systémique Appliquée aux Ruminants, INRA, AgroParisTech, Université Paris-Saclay, Paris, France
- * E-mail:
| | - Milka Popova
- Institute National de la Recherche Agronomique, UMR1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores, Clermont-Ferrand, France
| | - Maxence Tillier
- Institute National de la Recherche Agronomique, UMR1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores, Clermont-Ferrand, France
| | - Diego P. Morgavi
- Institute National de la Recherche Agronomique, UMR1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores, Clermont-Ferrand, France
| | | | - Gérard Fonty
- Université Clermont Auvergne, CNRS, LMGE, Clermont-Ferrand, France
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15
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Lan W, Yang C. Ruminal methane production: Associated microorganisms and the potential of applying hydrogen-utilizing bacteria for mitigation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 654:1270-1283. [PMID: 30841400 DOI: 10.1016/j.scitotenv.2018.11.180] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/12/2018] [Accepted: 11/12/2018] [Indexed: 05/16/2023]
Abstract
Methane emission from ruminants not only causes serious environmental problems, but also represents a significant source of energy loss to animals. The increasing demand for sustainable animal production is driving researchers to explore proper strategies to mitigate ruminal methanogenesis. Since hydrogen is the primary substrate of ruminal methanogenesis, hydrogen metabolism and its associated microbiome in the rumen may closely relate to low- and high-methane phenotypes. Using candidate microbes that can compete with methanogens and redirect hydrogen away from methanogenesis as ruminal methane mitigants are promising avenues for methane mitigation, which can both prevent the adverse effects deriving from chemical additives such as toxicity and resistance, and increase the retention of feed energy. This review describes the ruminal microbial ecosystem and its association with methane production, as well as the effects of interspecies hydrogen transfer on methanogenesis. It provides a scientific perspective on using bacteria that are involved in hydrogen utilization as ruminal modifiers to decrease methanogenesis. This information will be helpful in better understanding the key role of ruminal microbiomes and their relationship with methane production and, therefore, will form the basis of valuable and eco-friendly methane mitigation methods while improving animal productivity.
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Affiliation(s)
- Wei Lan
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China; MoE Key Laboratory of Molecular Animal Nutrition, China
| | - Chunlei Yang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China; MoE Key Laboratory of Molecular Animal Nutrition, China.
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16
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Ishaq SL, AlZahal O, Walker N, McBride B. An Investigation into Rumen Fungal and Protozoal Diversity in Three Rumen Fractions, during High-Fiber or Grain-Induced Sub-Acute Ruminal Acidosis Conditions, with or without Active Dry Yeast Supplementation. Front Microbiol 2017; 8:1943. [PMID: 29067009 PMCID: PMC5641310 DOI: 10.3389/fmicb.2017.01943] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 09/21/2017] [Indexed: 01/08/2023] Open
Abstract
Sub-acute ruminal acidosis (SARA) is a gastrointestinal functional disorder in livestock characterized by low rumen pH, which reduces rumen function, microbial diversity, host performance, and host immune function. Dietary management is used to prevent SARA, often with yeast supplementation as a pH buffer. Almost nothing is known about the effect of SARA or yeast supplementation on ruminal protozoal and fungal diversity, despite their roles in fiber degradation. Dairy cows were switched from a high-fiber to high-grain diet abruptly to induce SARA, with and without active dry yeast (ADY, Saccharomyces cerevisiae) supplementation, and sampled from the rumen fluid, solids, and epimural fractions to determine microbial diversity using the protozoal 18S rRNA and the fungal ITS1 genes via Illumina MiSeq sequencing. Diet-induced SARA dramatically increased the number and abundance of rare fungal taxa, even in fluid fractions where total reads were very low, and reduced protozoal diversity. SARA selected for more lactic-acid utilizing taxa, and fewer fiber-degrading taxa. ADY treatment increased fungal richness (OTUs) but not diversity (Inverse Simpson, Shannon), but increased protozoal richness and diversity in some fractions. ADY treatment itself significantly (P < 0.05) affected the abundance of numerous fungal genera as seen in the high-fiber diet: Lewia, Neocallimastix, and Phoma were increased, while Alternaria, Candida Orpinomyces, and Piromyces spp. were decreased. Likewise, for protozoa, ADY itself increased Isotricha intestinalis but decreased Entodinium furca spp. Multivariate analyses showed diet type was most significant in driving diversity, followed by yeast treatment, for AMOVA, ANOSIM, and weighted UniFrac. Diet, ADY, and location were all significant factors for fungi (PERMANOVA, P = 0.0001, P = 0.0452, P = 0.0068, Monte Carlo correction, respectively, and location was a significant factor (P = 0.001, Monte Carlo correction) for protozoa. Diet-induced SARA shifts diversity of rumen fungi and protozoa and selects against fiber-degrading species. Supplementation with ADY mitigated this reduction in protozoa, presumptively by triggering microbial diversity shifts (as seen even in the high-fiber diet) that resulted in pH stabilization. ADY did not recover the initial community structure that was seen in pre-SARA conditions.
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Affiliation(s)
| | | | | | - Brian McBride
- Animal Biosciences, University of Guelph, Guelph, ON, Canada
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17
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Han R, Zhang X, Liu J, Long Q, Chen L, Liu D, Zhu D. Microbial community structure and diversity within hypersaline Keke Salt Lake environments. Can J Microbiol 2017; 63:895-908. [PMID: 28850799 DOI: 10.1139/cjm-2016-0773] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Keke Salt Lake is located in the Qaidamu Basin of China. It is a unique magnesium sulfate-subtype hypersaline lake that exhibits a halite domain ecosystem, yet its microbial diversity has remained unstudied. Here, the microbial community structure and diversity was investigated via high-throughput sequencing of the V3-V5 regions of 16S rRNA genes. A high diversity of operational taxonomic units was detected for Bacteria and Archaea (734 and 747, respectively), comprising 21 phyla, 43 classes, and 201 genera of Bacteria and 4 phyla, 4 classes, and 39 genera of Archaea. Salt-saturated samples were dominated by the bacterial genera Bacillus (51.52%-58.35% relative abundance), Lactococcus (9.52%-10.51%), and Oceanobacillus (8.82%-9.88%) within the Firmicutes phylum (74.81%-80.99%), contrasting with other hypersaline lakes. The dominant Archaea belonged to the Halobacteriaceae family, and in particular, the genera (with an abundance of >10% of communities) Halonotius, Halorubellus, Halapricum, Halorubrum, and Natronomonas. Additionally, we report the presence of Nanohaloarchaeota and Woesearchaeota in Qinghai-Tibet Plateau lakes, which has not been previously documented. Total salinity (especially Mg2+, Cl-, Na+, and K+) mostly correlated with taxonomic distribution across samples. These results expand our understanding of microbial resource utilization within hypersaline lakes and the potential adaptations of dominant microorganisms that allow them to inhabit such environments.
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Affiliation(s)
- Rui Han
- a Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China.,b Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai 810016, People's Republic of China
| | - Xin Zhang
- c Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai 810016, People's Republic of China
| | - Jing Liu
- c Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai 810016, People's Republic of China
| | - Qifu Long
- c Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai 810016, People's Republic of China
| | - Laisheng Chen
- b Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai 810016, People's Republic of China
| | - Deli Liu
- a Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Derui Zhu
- c Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai 810016, People's Republic of China
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18
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Li XX, Liu JF, Zhou L, Mbadinga SM, Yang SZ, Gu JD, Mu BZ. Diversity and Composition of Sulfate-Reducing Microbial Communities Based on Genomic DNA and RNA Transcription in Production Water of High Temperature and Corrosive Oil Reservoir. Front Microbiol 2017. [PMID: 28638372 PMCID: PMC5461352 DOI: 10.3389/fmicb.2017.01011] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Deep subsurface petroleum reservoir ecosystems harbor a high diversity of microorganisms, and microbial influenced corrosion is a major problem for the petroleum industry. Here, we used high-throughput sequencing to explore the microbial communities based on genomic 16S rDNA and metabolically active 16S rRNA analyses of production water samples with different extents of corrosion from a high-temperature oil reservoir. Results showed that Desulfotignum and Roseovarius were the most abundant genera in both genomic and active bacterial communities of all the samples. Both genomic and active archaeal communities were mainly composed of Archaeoglobus and Methanolobus. Within both bacteria and archaea, the active and genomic communities were compositionally distinct from one another across the different oil wells (bacteria p = 0.002; archaea p = 0.01). In addition, the sulfate-reducing microorganisms (SRMs) were specifically assessed by Sanger sequencing of functional genes aprA and dsrA encoding the enzymes adenosine-5'-phosphosulfate reductase and dissimilatory sulfite reductase, respectively. Functional gene analysis indicated that potentially active Archaeoglobus, Desulfotignum, Desulfovibrio, and Thermodesulforhabdus were frequently detected, with Archaeoglobus as the most abundant and active sulfate-reducing group. Canonical correspondence analysis revealed that the SRM communities in petroleum reservoir system were closely related to pH of the production water and sulfate concentration. This study highlights the importance of distinguishing the metabolically active microorganisms from the genomic community and extends our knowledge on the active SRM communities in corrosive petroleum reservoirs.
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Affiliation(s)
- Xiao-Xiao Li
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and TechnologyShanghai, China
| | - Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and TechnologyShanghai, China
| | - Lei Zhou
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and TechnologyShanghai, China
| | - Serge M Mbadinga
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and TechnologyShanghai, China.,Shanghai Collaborative Innovation Center for Biomanufacturing TechnologyShanghai, China
| | - Shi-Zhong Yang
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and TechnologyShanghai, China
| | - Ji-Dong Gu
- School of Biological Sciences, The University of Hong KongHong Kong, Hong Kong
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and TechnologyShanghai, China.,Shanghai Collaborative Innovation Center for Biomanufacturing TechnologyShanghai, China
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19
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Investigation and manipulation of metabolically active methanogen community composition during rumen development in black goats. Sci Rep 2017; 7:422. [PMID: 28341835 PMCID: PMC5428682 DOI: 10.1038/s41598-017-00500-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 02/28/2017] [Indexed: 01/08/2023] Open
Abstract
This study was performed to investigate the initial colonization of metabolically active methanogens and subsequent changes in four fractions: the rumen solid-phase (RS), liquid-phase (RL), protozoa-associated (RP), and epithelium-associated (RE) from 1 to 60 d after birth, and manipulate methanogen community by early weaning on 40 d and supplementing rhubarb from 40 to 60 d in black goats. The RNA-based real-time quantitative PCR and 16S rRNA amplicon sequencing were employed to indicate the metabolically active methanogens. Results showed that active methanogens colonized in RL and RE on 1 d after birth. RP and RE contained the highest and lowest density of methanogens, respectively. Methanobrevibacter, Candidatus Methanomethylophilus, and Methanosphaera were the top three genera. The methanogen communities before weaning differed from those post weaning and the structure of the methanogen community in RE was distinct from those in the other three fractions. The discrepancies in the distribution of methanogens across four fractions, and various fluctuations in abundances among four fractions according to age were observed. The addition of rhubarb significantly (P < 0.05) reduced the abundances of Methanimicrococcus spp. in four fractions on 50 d, but did not change the methanogen community composition on 60 d.
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20
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Patra A, Park T, Kim M, Yu Z. Rumen methanogens and mitigation of methane emission by anti-methanogenic compounds and substances. J Anim Sci Biotechnol 2017; 8:13. [PMID: 28149512 PMCID: PMC5270371 DOI: 10.1186/s40104-017-0145-9] [Citation(s) in RCA: 213] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 01/13/2017] [Indexed: 11/25/2022] Open
Abstract
Methanogenic archaea reside primarily in the rumen and the lower segments of the intestines of ruminants, where they utilize the reducing equivalents derived from rumen fermentation to reduce carbon dioxide, formic acid, or methylamines to methane (CH4). Research on methanogens in the rumen has attracted great interest in the last decade because CH4 emission from ruminants contributes to global greenhouse gas emission and represents a loss of feed energy. Some DNA-based phylogenetic studies have depicted a diverse and dynamic community of methanogens in the rumen. In the past decade, researchers have focused on elucidating the underpinning that determines and affects the diversity, composition, structure, and dynamics of methanogen community of the rumen. Concurrently, many researchers have attempted to develop and evaluate interventions to mitigate enteric CH4 emission. Although much work has been done using plant secondary metabolites, other approaches such as using nitrate and 3-nitrooxy propanol have also yielded promising results. Most of these antimethanogenic compounds or substances often show inconsistent results among studies and also lead to adverse effects on feed intake and digestion and other aspects of rumen fermentation when fed at doses high enough to achieve effective mitigation. This review provides a brief overview of the rumen methanogens and then an appraisal of most of the antimethanogenic compounds and substances that have been evaluated both in vitro and in vivo. Knowledge gaps and future research needs are also discussed with a focus on methanogens and methane mitigation.
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Affiliation(s)
- Amlan Patra
- Department of Animal Sciences, The Ohio State University, 2029 Fyffe Road, Columbus, OH 43210 USA.,Department of Animal Nutrition, West Bengal University of Animal and Fishery Sciences, 37 K. B. Sarani, Belgachia, Kolkata, 700037 India
| | - Tansol Park
- Department of Animal Sciences, The Ohio State University, 2029 Fyffe Road, Columbus, OH 43210 USA
| | - Minseok Kim
- Animal Nutrition and Physiology Team, National Institute of Animal Science, Rural Development Administration, Wanju, 55365 Republic of Korea
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, 2029 Fyffe Road, Columbus, OH 43210 USA
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21
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Metabolic adaptations to HFHS overfeeding: how whole body and tissues postprandial metabolic flexibility adapt in Yucatan mini-pigs. Eur J Nutr 2016; 57:119-135. [PMID: 27568059 DOI: 10.1007/s00394-016-1302-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 08/16/2016] [Indexed: 12/18/2022]
Abstract
PURPOSE In the present study, we aimed to metabolically characterize the postprandial adaptations of the major tissues involved in energy, lipids and amino acids metabolisms in mini-pigs. METHOD Mini-pigs were fed on high-fat-high-sucrose (HFHS) diet for 2 months and several tissues explored for metabolic analyses. Further, the urine metabolome was followed over the time to picture the metabolic adaptations occurring at the whole body level following overfeeding. RESULTS After 2 months of HFHS consumption, mini-pigs displayed an obese phenotype characterized by high circulating insulin, triglycerides and cholesterol levels. At the tissue level, a general (muscle, adipose tissue, intestine) reduction in the capacity to phosphorylate glucose was observed. This was also supported by the enhanced hepatic gluconeogenesis potential, despite the concomitant normoglycaemia, suggesting that the high circulating insulin levels would be enough to maintain glucose homoeostasis. The HFHS feeding also resulted in a reduced capacity of two other pathways: the de novo lipogenesis, and the branched-chain amino acids transamination. Finally, the follow-up of the urine metabolome over the time allowed determining breaking points in the metabolic trajectory of the animals. CONCLUSIONS Several features confirmed the pertinence of the animal model, including increased body weight, adiposity and porcine obesity index. At the metabolic level, we observed a perturbed glucose and amino acid metabolism, known to be related to the onset of the obesity. The urine metabolome analyses revealed several metabolic pathways potentially involved in the obesity onset, including TCA (citrate, pantothenic acid), amino acids catabolism (cysteine, threonine, leucine).
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Wang P, Zhao S, Wang X, Zhang Y, Zheng N, Wang J. Ruminal Methanogen Community in Dairy Cows Fed Agricultural Residues of Corn Stover, Rapeseed, and Cottonseed Meals. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:5439-5445. [PMID: 27322573 DOI: 10.1021/acs.jafc.6b00708] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The purpose was to reveal changes in the methanogen community in the rumen of dairy cows fed agricultural residues of corn stover, rapeseed, and cottonseed meals, compared with alfalfa hay or soybean meal. Analysis was based on cloning and sequencing the methyl coenzyme M reductase α-subunit gene of ruminal methanogens. Results revealed that predicted methane production was increased while population of ruminal methanogens was not significantly affected when cows were fed diets containing various amounts of agricultural residues. Richness and diversity of methanogen community were markedly increased by addition of agricultural residues. The dominant ruminal methanogens shared by all experimental groups belonged to rumen cluster C, accounting for 71% of total, followed by the order Methanobacteriales (29%). Alterations of ruminal methanogen community and prevalence of particular species occurred in response to fed agricultural residue rations, suggesting the possibility of regulating target methanogens to control methane production by dairy cows fed agricultural residues.
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Affiliation(s)
- Pengpeng Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Laboratory of Quality & Safety Risk Assessment for Dairy Products of Ministry of Agriculture (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Milk and Dairy Production Inspection Center of Ministry of Agriculture (Beijing) , Beijing, 100193, People's Republic of China
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Laboratory of Quality & Safety Risk Assessment for Dairy Products of Ministry of Agriculture (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Milk and Dairy Production Inspection Center of Ministry of Agriculture (Beijing) , Beijing, 100193, People's Republic of China
| | - Xingwen Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Laboratory of Quality & Safety Risk Assessment for Dairy Products of Ministry of Agriculture (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Milk and Dairy Production Inspection Center of Ministry of Agriculture (Beijing) , Beijing, 100193, People's Republic of China
| | - Yangdong Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Laboratory of Quality & Safety Risk Assessment for Dairy Products of Ministry of Agriculture (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Milk and Dairy Production Inspection Center of Ministry of Agriculture (Beijing) , Beijing, 100193, People's Republic of China
| | - Nan Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Laboratory of Quality & Safety Risk Assessment for Dairy Products of Ministry of Agriculture (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Milk and Dairy Production Inspection Center of Ministry of Agriculture (Beijing) , Beijing, 100193, People's Republic of China
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Laboratory of Quality & Safety Risk Assessment for Dairy Products of Ministry of Agriculture (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Milk and Dairy Production Inspection Center of Ministry of Agriculture (Beijing) , Beijing, 100193, People's Republic of China
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Hirakata Y, Oshiki M, Kuroda K, Hatamoto M, Kubota K, Yamaguchi T, Harada H, Araki N. Effects of Predation by Protists on Prokaryotic Community Function, Structure, and Diversity in Anaerobic Granular Sludge. Microbes Environ 2016; 31:279-87. [PMID: 27431197 PMCID: PMC5017804 DOI: 10.1264/jsme2.me16067] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Predation by protists is top-down pressure that regulates prokaryotic abundance, community function, structure, and diversity in natural and artificial ecosystems. Although the effects of predation by protists have been studied in aerobic ecosystems, they are poorly understood in anoxic environments. We herein studied the influence of predation by Metopus and Caenomorpha ciliates—ciliates frequently found in anoxic ecosystems—on prokaryotic community function, structure, and diversity. Metopus and Caenomorpha ciliates were cocultivated with prokaryotic assemblages (i.e., anaerobic granular sludge) in an up-flow anaerobic sludge blanket (UASB) reactor for 171 d. Predation by these ciliates increased the methanogenic activities of granular sludge, which constituted 155% of those found in a UASB reactor without the ciliates (i.e., control reactor). Sequencing of 16S rRNA gene amplicons using Illumina MiSeq revealed that the prokaryotic community in the UASB reactor with the ciliates was more diverse than that in the control reactor; 2,885–3,190 and 2,387–2,426 operational taxonomic units (>97% sequence similarities), respectively. The effects of predation by protists in anaerobic engineered systems have mostly been overlooked, and our results show that the influence of predation by protists needs to be examined and considered in the future for a better understanding of prokaryotic community structure and function.
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Affiliation(s)
- Yuga Hirakata
- Department of Civil Engineering, National Institute of Technology, Nagaoka College
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24
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Li F, Henderson G, Sun X, Cox F, Janssen PH, Guan LL. Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches. Front Microbiol 2016; 7:987. [PMID: 27446027 PMCID: PMC4916217 DOI: 10.3389/fmicb.2016.00987] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/08/2016] [Indexed: 12/20/2022] Open
Abstract
Taxonomic characterization of active gastrointestinal microbiota is essential to detect shifts in microbial communities and functions under various conditions. This study aimed to identify and quantify potentially active rumen microbiota using total RNA sequencing and to compare the outcomes of this approach with the widely used targeted RNA/DNA amplicon sequencing technique. Total RNA isolated from rumen digesta samples from five beef steers was subjected to Illumina paired-end sequencing (RNA-seq), and bacterial and archaeal amplicons of partial 16S rRNA/rDNA were subjected to 454 pyrosequencing (RNA/DNA Amplicon-seq). Taxonomic assessments of the RNA-seq, RNA Amplicon-seq, and DNA Amplicon-seq datasets were performed using a pipeline developed in house. The detected major microbial phylotypes were common among the three datasets, with seven bacterial phyla, fifteen bacterial families, and five archaeal taxa commonly identified across all datasets. There were also unique microbial taxa detected in each dataset. Elusimicrobia and Verrucomicrobia phyla; Desulfovibrionaceae, Elusimicrobiaceae, and Sphaerochaetaceae families; and Methanobrevibacter woesei were only detected in the RNA-Seq and RNA Amplicon-seq datasets, whereas Streptococcaceae was only detected in the DNA Amplicon-seq dataset. In addition, the relative abundances of four bacterial phyla, eight bacterial families and one archaeal taxon were different among the three datasets. This is the first study to compare the outcomes of rumen microbiota profiling between RNA-seq and RNA/DNA Amplicon-seq datasets. Our results illustrate the differences between these methods in characterizing microbiota both qualitatively and quantitatively for the same sample, and so caution must be exercised when comparing data.
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Affiliation(s)
- Fuyong Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta Edmonton, AB, Canada
| | - Gemma Henderson
- AgResearch Ltd., Grasslands Research Centre Palmerston North, New Zealand
| | - Xu Sun
- Department of Agricultural, Food and Nutritional Science, University of Alberta Edmonton, AB, Canada
| | - Faith Cox
- AgResearch Ltd., Grasslands Research Centre Palmerston North, New Zealand
| | - Peter H Janssen
- AgResearch Ltd., Grasslands Research Centre Palmerston North, New Zealand
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta Edmonton, AB, Canada
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Ramírez-Restrepo CA, Tan C, ONeill CJ, López-Villalobos N, Padmanabha J, Wang J, McSweeney CS. Methane production, fermentation characteristics, and microbial profiles in the rumen of tropical cattle fed tea seed saponin supplementation. Anim Feed Sci Technol 2016. [DOI: 10.1016/j.anifeedsci.2016.03.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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26
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Oh J, Hristov AN. Effects of Plant-Derived Bio-Active Compounds on Rumen Fermentation, Nutrient Utilization, Immune Response, and Productivity of Ruminant Animals. ACS SYMPOSIUM SERIES 2016. [DOI: 10.1021/bk-2016-1218.ch011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- J. Oh
- Department of Animal Science, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - A. N. Hristov
- Department of Animal Science, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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Newbold CJ, de la Fuente G, Belanche A, Ramos-Morales E, McEwan NR. The Role of Ciliate Protozoa in the Rumen. Front Microbiol 2015; 6:1313. [PMID: 26635774 PMCID: PMC4659874 DOI: 10.3389/fmicb.2015.01313] [Citation(s) in RCA: 308] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 11/09/2015] [Indexed: 01/17/2023] Open
Abstract
First described in 1843, Rumen protozoa with their striking appearance were assumed to be important for the welfare of their host. However, despite contributing up to 50% of the bio-mass in the rumen, the role of protozoa in rumen microbial ecosystem remains unclear. Phylogenetic analysis of 18S rDNA libraries generated from the rumen of cattle, sheep, and goats has revealed an unexpected diversity of ciliated protozoa although variation in gene copy number between species makes it difficult to obtain absolute quantification. Despite repeated attempts it has proven impossible to maintain rumen protozoa in axenic culture. Thus it has been difficult to establish conclusively a role of ciliate protozoa in rumen fiber degradation. The development of techniques to clone and express ciliate genes in λ phage, together with bioinformatic indices to confirm the ciliate origin of the genes has allowed the isolation and characterization of fibrolytic genes from rumen protozoa. Elimination of the ciliate protozoa increases microbial protein supply by up to 30% and reduces methane production by up to 11%. Our recent findings suggest that holotrich protozoa play a disproportionate role in supporting methanogenesis whilst the small Entodinium are responsible for much of the bacterial protein turnover. As yet no method to control protozoa in the rumen that is safe and practically applicable has been developed, however a range of plant extract capable of controlling if not completely eliminating rumen protozoa have been described.
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Affiliation(s)
- Charles J. Newbold
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Gabriel de la Fuente
- Departament de Producció Animal, Escola Tècnica Superior d’Enginyeria Agrària, Universitat de Lleida, Lleida, Spain
| | - Alejandro Belanche
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Eva Ramos-Morales
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Neil R. McEwan
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
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Ishaq SL, Sundset MA, Crouse J, Wright ADG. High-throughput DNA sequencing of the moose rumen from different geographical locations reveals a core ruminal methanogenic archaeal diversity and a differential ciliate protozoal diversity. Microb Genom 2015; 1:e000034. [PMID: 28348818 PMCID: PMC5320624 DOI: 10.1099/mgen.0.000034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/05/2015] [Accepted: 09/15/2015] [Indexed: 12/13/2022] Open
Abstract
Moose rumen samples from Vermont, Alaska and Norway were investigated for methanogenic archaeal and protozoal density using real-time PCR, and diversity using high-throughput sequencing of the 16S and 18S rRNA genes. Vermont moose showed the highest protozoal and methanogen densities. Alaskan samples had the highest percentages of Methanobrevibacter smithii, followed by the Norwegian samples. One Norwegian sample contained 43 % Methanobrevibacter thaueri, whilst all other samples contained < 10 %. Vermont samples had large percentages of Methanobrevibacter ruminantium, as did two Norwegian samples. Methanosphaera stadtmanae represented one-third of sequences in three samples. Samples were heterogeneous based on gender, geographical location and weight class using analysis of molecular variance (AMOVA). Two Alaskan moose contained >70 % Polyplastron multivesiculatum and one contained >75 % Entodinium spp. Protozoa from Norwegian moose belonged predominantly (>50 %) to the genus Entodinium, especially Entodinium caudatum. Norwegian moose contained a large proportion of sequences (25–97 %) which could not be classified beyond family. Protozoa from Vermont samples were predominantly Eudiplodinium rostratum (>75 %), with up to 7 % Diploplastron affine. Four of the eight Vermont samples also contained 5–12 % Entodinium spp. Samples were heterogeneous based on AMOVA, principal coordinate analysis and UniFrac. This study gives the first insight into the methanogenic archaeal diversity in the moose rumen. The high percentage of rumen archaeal species associated with high starch diets found in Alaskan moose corresponds well to previous data suggesting that they feed on plants high in starch. Similarly, the higher percentage of species related to forage diets in Vermont moose also relates well to their higher intake of fibre.
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Affiliation(s)
- Suzanne L Ishaq
- Department of Animal Science, University of Vermont, Burlington, Vermont, USA.,Department of Animal and Range Science, Montana State University, Bozeman, Montana, USA
| | - Monica A Sundset
- Department of Arctic and Marine Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway, USA
| | - John Crouse
- Alaska Department of Fish and Game, Soldotna, Alaska, USA
| | - André-Denis G Wright
- Department of Animal Science, University of Vermont, Burlington, Vermont, USA.,School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, USA
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29
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Bayat AR, Kairenius P, Stefański T, Leskinen H, Comtet-Marre S, Forano E, Chaucheyras-Durand F, Shingfield KJ. Effect of camelina oil or live yeasts (Saccharomyces cerevisiae) on ruminal methane production, rumen fermentation, and milk fatty acid composition in lactating cows fed grass silage diets. J Dairy Sci 2015; 98:3166-81. [PMID: 25726099 DOI: 10.3168/jds.2014-7976] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 01/14/2015] [Indexed: 11/19/2022]
Abstract
The potential of dietary supplements of 2 live yeast strains (Saccharomyces cerevisiae) or camelina oil to lower ruminal methane (CH4) and carbon dioxide (CO2) production and the associated effects on animal performance, rumen fermentation, rumen microbial populations, nutrient metabolism, and milk fatty acid (FA) composition of cows fed grass silage-based diets were examined. Four Finnish Ayrshire cows (53±7 d in milk) fitted with rumen cannula were used in a 4×4 Latin square with four 42-d periods. Cows received a basal total mixed ration (control treatment) with a 50:50 forage-to-concentrate ratio [on a dry matter (DM) basis] containing grass silage, the same basal total mixed ration supplemented with 1 of 2 live yeasts, A or B, administered directly in the rumen at 10(10) cfu/d (treatments A and B), or supplements of 60g of camelina oil/kg of diet DM that replaced concentrate ingredients in the basal total mixed ration (treatment CO). Relative to the control, treatments A and B had no effects on DM intake, rumen fermentation, ruminal gas production, or apparent total-tract nutrient digestibility. In contrast, treatment CO lowered DM intake and ruminal CH4 and CO2 production, responses associated with numerical nonsignificant decreases in total-tract organic matter digestibility, but no alterations in rumen fermentation characteristics or changes in the total numbers of rumen bacteria, methanogens, protozoa, and fungi. Compared with the control, treatment CO decreased the yields of milk, milk fat, lactose, and protein. Relative to treatment B, treatment CO improved nitrogen utilization due to a lower crude protein intake. Treatment A had no influence on milk FA composition, whereas treatment B increased cis-9 10:1 and decreased 11-cyclohexyl 11:0 and 24:0 concentrations. Treatment CO decreased milk fat 8:0 to 16:0 and total saturated FA, and increased 18:0, 18:1, 18:2, conjugated linoleic acid, 18:3n-3, and trans FA concentrations. Decreases in ruminal CH4 production to treatment CO were related, at least in part to lowered DM intake, whereas treatments had no effect on ruminal CH4 emission intensity (g/kg of digestible organic matter intake or milk yield). Results indicated that live yeasts A and B had no influence on animal performance, ruminal gas production, rumen fermentation, or nutrient utilization in cows fed grass silage-based diets. Dietary supplements of camelina oil decreased ruminal CH4 and CO2 production, but also lowered the yields of milk and milk constituents due to an adverse effect on intake.
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Affiliation(s)
- A R Bayat
- Nutritional Physiology, Green Technology, Natural Resources Institute Finland (Luke), FI 31600, Jokioinen, Finland.
| | - P Kairenius
- Nutritional Physiology, Green Technology, Natural Resources Institute Finland (Luke), FI 31600, Jokioinen, Finland
| | - T Stefański
- Nutritional Physiology, Green Technology, Natural Resources Institute Finland (Luke), FI 31600, Jokioinen, Finland
| | - H Leskinen
- Nutritional Physiology, Green Technology, Natural Resources Institute Finland (Luke), FI 31600, Jokioinen, Finland
| | - S Comtet-Marre
- INRA, Microbiology unit UR454, CR Clermont Ferrand/Theix, 63122 St-Genes-Champanelle, France
| | - E Forano
- INRA, Microbiology unit UR454, CR Clermont Ferrand/Theix, 63122 St-Genes-Champanelle, France
| | - F Chaucheyras-Durand
- INRA, Microbiology unit UR454, CR Clermont Ferrand/Theix, 63122 St-Genes-Champanelle, France; Lallemand Animal Nutrition, 19 rue des Briquetiers, BP59, 31702 Blagnac Cedex, France
| | - K J Shingfield
- Nutritional Physiology, Green Technology, Natural Resources Institute Finland (Luke), FI 31600, Jokioinen, Finland
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Belanche A, de la Fuente G, Newbold CJ. Effect of progressive inoculation of fauna-free sheep with holotrich protozoa and total-fauna on rumen fermentation, microbial diversity and methane emissions. FEMS Microbiol Ecol 2014; 91:fiu026. [PMID: 25764558 PMCID: PMC4399445 DOI: 10.1093/femsec/fiu026] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Rumen methanogenesis represents an energy waste for the ruminant and an important source of greenhouse gas; thus, integrated studies are needed to fully understand this process. Eight fauna-free sheep were used to investigate the effect of successive inoculation with holotrich protozoa then with total fauna on rumen methanogenesis. Holotrichs inoculation neither altered rumen fermentation rate nor diet digestibility, but increased concentrations of acetate (+15%), butyrate (+57%), anaerobic fungi (+0.82 log), methanogens (+0.41 log) and methanogenesis (+54%). Further inoculation with total fauna increased rumen concentrations of protozoa (+1.0 log), bacteria (+0.29 log), anaerobic fungi (+0.78 log), VFA (+8%), ammonia and fibre digestibility (+17%) without affecting levels of methanogens or methanogenesis. Rumen methanogens population was fairly stable in terms of structure and diversity, while the bacterial community was highly affected by the treatments. Inoculation with holotrich protozoa increased bacterial diversity. Further inoculation with total fauna lowered bacterial diversity but increased concentrations of certain propionate and lactate-producing bacteria, suggesting that alternative H2 sinks could be relevant. This experiment suggests that holotrich protozoa have a greater impact on rumen methanogenesis than entodiniomorphids. Thus, further research is warranted to understand the effect of holotrich protozoa on methane formation and evaluate their elimination from the rumen as a potential methane mitigation strategy.
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Affiliation(s)
- Alejandro Belanche
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion SY23 3DB, UK
| | - Gabriel de la Fuente
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion SY23 3DB, UK
| | - Charles J Newbold
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion SY23 3DB, UK
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Belanche A, de la Fuente G, Newbold CJ. Study of methanogen communities associated with different rumen protozoal populations. FEMS Microbiol Ecol 2014; 90:663-77. [PMID: 25195951 PMCID: PMC4286163 DOI: 10.1111/1574-6941.12423] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 09/01/2014] [Accepted: 09/02/2014] [Indexed: 01/17/2023] Open
Abstract
Protozoa-associated methanogens (PAM) are considered one of the most active communities in the rumen methanogenesis. This experiment investigated whether methanogens are sequestrated within rumen protozoa, and structural differences between rumen free-living methanogens and PAM. Rumen protozoa were harvested from totally faunated sheep, and six protozoal fractions (plus free-living microorganisms) were generated by sequential filtration. Holotrich-monofaunated sheep were also used to investigate the holotrich-associated methanogens. Protozoal size determined the number of PAM as big protozoa had 1.7–3.3 times more methanogen DNA than smaller protozoa, but also more endosymbiotic bacteria (2.2- to 3.5-fold times). Thus, similar abundance of methanogens with respect to total bacteria were observed across all protozoal fractions and free-living microorganisms, suggesting that methanogens are not accumulated within rumen protozoa in a greater proportion to that observed in the rumen as a whole. All rumen methanogen communities had similar diversity (22.2 ± 3.4 TRFs). Free-living methanogens composed a conserved community (67% similarity within treatment) in the rumen with similar diversity but different structures than PAM (P < 0.05). On the contrary, PAM constituted a more variable community (48% similarity), which differed between holotrich and total protozoa (P < 0.001). Thus, PAM constitutes a community, which requires further investigation as part of methane mitigation strategies.
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Affiliation(s)
- Alejandro Belanche
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
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Zhang Y, Chen L, Sun R, Dai T, Tian J, Liu R, Wen D. Effect of wastewater disposal on the bacterial and archaeal community of sea sediment in an industrial area in China. FEMS Microbiol Ecol 2014; 88:320-32. [DOI: 10.1111/1574-6941.12298] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 02/03/2014] [Accepted: 02/04/2014] [Indexed: 11/26/2022] Open
Affiliation(s)
- Yan Zhang
- School of Environment; Tsinghua University; Beijing China
| | - Lujun Chen
- School of Environment; Tsinghua University; Beijing China
- Zhejiang Provincial Key Laboratory of Water Science and Technology; Department of Environmental Technology and Ecology; Yangtze Delta Region Institute of Tsinghua University; Zhejiang Jiaxing China
| | - Renhua Sun
- College of Environmental Sciences and Engineering; Peking University; Beijing China
| | - Tianjiao Dai
- College of Environmental Sciences and Engineering; Peking University; Beijing China
| | - Jinping Tian
- School of Environment; Tsinghua University; Beijing China
| | - Rui Liu
- Zhejiang Provincial Key Laboratory of Water Science and Technology; Department of Environmental Technology and Ecology; Yangtze Delta Region Institute of Tsinghua University; Zhejiang Jiaxing China
| | - Donghui Wen
- College of Environmental Sciences and Engineering; Peking University; Beijing China
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Li ZP, Liu HL, Jin CA, Cui XZ, Jing Y, Yang FH, Li GY, Wright ADG. Differences in the methanogen population exist in sika deer (Cervus nippon) fed different diets in China. MICROBIAL ECOLOGY 2013; 66:879-888. [PMID: 24061342 DOI: 10.1007/s00248-013-0282-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 08/21/2013] [Indexed: 06/02/2023]
Abstract
Understanding the methanogen structure from sika deer (Cervus nippon) in China may be beneficial to methane mitigation. In the present preliminary study, we investigated the methanogen community in the rumen of domesticated sika deer fed either tannin-rich plants (oak leaf, OL group) or corn stalk (CS group) using 16S rRNA gene clone libraries. Overall, we obtained 197 clone sequences, revealing 146 unique phylotypes, which were assigned to 36 operational taxonomic units at the species level (98 % identity). Methanogens related to the genus Methanobrevibacter were the predominant phylotypes representing 83.9 % (OL library) and 85.9 % (CS library) of the clones. Methanobrevibacter millerae was the most abundant species in both libraries, but the proportion of M. millerae-related clones in the CS library was higher than in the OL library (69.5 and 51.4 %, respectively). Moreover, Methanobrevibacter wolinii-related clones (32.5 %) were predominant in the OL library. Methanobrevibacter smithii-related clones and Methanobrevibacter ruminantium-related clones accounted for 6.5 and 6.6 % in the CS library, respectively. However, these clones were absent from the OL library. The concentrations of butyrate and total short-chain fatty acids (SCFAs) were significantly higher in the OL group, but the concentrations of acetate, propionate, and valerate and the acetate to propionate ratio in the OL group were not significantly different between the two groups. Tannin-rich plants may have affected the distribution of genus Methanobrevibacter phylotypes at the species level and the concentration and composition of SCFAs.
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Affiliation(s)
- Zhi Peng Li
- Department of Economical Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Jilin, China
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Xia Y, Kong YH, Seviour R, Forster RJ, Kisidayova S, McAllister TA. Fluorescence in situ hybridization probing of protozoal Entodinium spp. and their methanogenic colonizers in the rumen of cattle fed alfalfa hay or triticale straw. J Appl Microbiol 2013; 116:14-22. [PMID: 24118832 DOI: 10.1111/jam.12356] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 07/12/2013] [Accepted: 09/23/2013] [Indexed: 11/30/2022]
Abstract
AIMS To develop and test a fluorescence in situ hybridization (FISH) based technique and to identify and quantify simultaneously those methanogenic populations colonizing Entodinium spp. in the rumen of cows fed different forages. METHODS AND RESULTS New FISH probes targeting protozoal Entodinium spp. were designed and used together with FISH probes for methanogens in the cow rumen. The composition and relative abundance of methanogenic populations colonizing Entodinium simplex-, E. caudaum- and Entodinium furca-related populations were similar. Methanogens including Methanobrevibacter thaueri, Methanobrevibacter millerae and Methanobrevibacter smithii, and members of Methanomicrobium and Methanosphaera were generally the predominant colonizers of protozoa, regardless of the forage fed to cattle. Individual animals appeared to differ in which ruminal methanogenic populations colonized each of the individual Entodinium spp. CONCLUSIONS Simultaneous FISH probing is shown here to be a reliable and effective approach to investigate the dynamics of symbiotic relationships between ruminal protozoa and methanogens at a single cell level. Phylogenetically closely related Entodinium spp. were colonized by similar methanogenic populations regardless of the forage fed. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report of the methanogenic archaeal populations that specifically colonize Entodinium spp. as identified using simultaneous FISH probing.
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Affiliation(s)
- Y Xia
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada; Department of Biological Science and Technology, Kunming University, Kunming, China
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Fernandes J, Wang A, Su W, Rozenbloom SR, Taibi A, Comelli EM, Wolever TMS. Age, dietary fiber, breath methane, and fecal short chain fatty acids are interrelated in Archaea-positive humans. J Nutr 2013; 143:1269-75. [PMID: 23739307 DOI: 10.3945/jn.112.170894] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Recent attention has focused on the significance of colonic Archaea in human health and energy metabolism. The main objectives of this study were to determine the associations among the number of fecal Archaea, body mass index (BMI), fecal short chain fatty acid (SCFA) concentrations, and dietary intakes of healthy humans. We collected demographic information, 3-d diet records, and breath and fecal samples from 95 healthy participants who were divided into 2 groups: detectable Archaea (>10(6) copies/g; Arch+ve) and undetectable Archaea. Dietary intakes, BMI, and fecal SCFAs were similar in both groups. The mean number of Archaea 16S rRNA gene copies detected in Arch+ve participants' feces was 8.9 ± 0.2 log/g wet weight. In Arch+ve participants, there were positive correlations between breath methane and age (r = 0.52; P = 0.001), total dietary fiber (TDF) intake (r = 0.57; P = 0.0003), and log number of fecal Archaea 16S rRNA gene copies (r = 0.35; P = 0.03). In the Arch+ve group, negative correlations were observed between TDF/1000 kcal and fecal total SCFA (r = -0.46; P ≤ 0.01) and between breath methane and fecal total SCFA (r = -0.42; P = 0.01). Principal component analysis identified a distinct Archaea factor with positive loadings of age, breath methane, TDF, TDF/1000 kcal, and number of log Archaea 16S rRNA gene copies. The results suggest that colonic Archaea is not associated with obesity in healthy humans. The presence of Archaea in humans may influence colonic fermentation by altering SCFA metabolism and fecal SCFA profile.
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Affiliation(s)
- Judlyn Fernandes
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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Yue ZB, Li WW, Yu HQ. Application of rumen microorganisms for anaerobic bioconversion of lignocellulosic biomass. BIORESOURCE TECHNOLOGY 2013; 128:738-744. [PMID: 23265823 DOI: 10.1016/j.biortech.2012.11.073] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 11/10/2012] [Accepted: 11/18/2012] [Indexed: 06/01/2023]
Abstract
Rumen in the mammalian animals is a natural cellulose-degrading system and the microorganisms inside have been found to be able to effectively digest lignocellulosic biomass. Furthermore, methane or volatile fatty acids, which could be further converted to other biofuels, are the two major products in such a system. This paper offers an overview of recent development in the application of rumen microorganisms for lignocellulosic biomass conversion. Application of recent molecular tools in the analysis of rumen microbial community, progress in the development of artificial rumen reactors, the latest research results about characterizing rumen-dominated anaerobic digestion process and energy products are summarized. Also, the potential application of such a rumen-dominated process is discussed.
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Affiliation(s)
- Zheng-Bo Yue
- School of Resources & Environmental Engineering, Hefei University of Technology, Hefei 230009, China
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38
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Zhou M, Hünerberg M, Beauchemin KA, McAllister TA, Okine EK, Guan LL. Individuality of ruminal methanogen/protozoa populations in beef cattle fed diets containing dried distillers' grain with solubles. ACTA AGR SCAND A-AN 2012. [DOI: 10.1080/09064702.2013.788206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Eugenol for dairy cows fed low or high concentrate diets: Effects on digestion, ruminal fermentation characteristics, rumen microbial populations and milk fatty acid profile. Anim Feed Sci Technol 2012. [DOI: 10.1016/j.anifeedsci.2012.10.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Gagen EJ, Mosoni P, Denman SE, Al Jassim R, McSweeney CS, Forano E. Methanogen colonisation does not significantly alter acetogen diversity in lambs isolated 17 h after birth and raised aseptically. MICROBIAL ECOLOGY 2012; 64:628-640. [PMID: 22383121 DOI: 10.1007/s00248-012-0024-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 02/03/2012] [Indexed: 05/31/2023]
Abstract
Reductive acetogenesis is not competitive with methanogenesis in adult ruminants, whereas acetogenic bacteria are the dominant hydrogenotrophs in the early rumen microbiota. The ecology of hydrogenotrophs in the developing rumen was investigated using young lambs, raised in sterile isolators, and conventional adult sheep. Two lambs were born naturally, left with their dams for 17 h and then placed into a sterile isolator and reared aseptically. They were inoculated with cellulolytic bacteria and later with Methanobrevibacter sp. 87.7 to investigate the effect of methanogen establishment on the rumen acetogen population since they lacked cultivable representatives of methanogens. Putative acetogens were investigated by acetyl-CoA synthase and formyltetrahydrofolate synthetase gene analysis and methanogens by methyl coenzyme reductase A gene analysis. Unexpectedly, a low abundant but diverse population of methanogens (predominantly Methanobrevibacter spp.) was identified in isolated lambs pre-inoculation with Mbb. sp 87.7, which was similar to the community structure in conventional sheep. In contrast, potential acetogen diversity in isolated lambs and conventional sheep was different. Potential acetogens affiliated between the Lachnospiraceae and Clostridiaceae in conventional sheep and with the Blautia genus and the Lachnospiraceae in isolated lambs. The establishment of Mbb. sp. 87.7 (1,000-fold increase in methanogens) did not substantially affect acetogen diversity.
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Affiliation(s)
- Emma J Gagen
- CSIRO Livestock Industries, St. Lucia, QLD 4067, Australia.
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41
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Hristov AN, Callaway TR, Lee C, Dowd SE. Rumen bacterial, archaeal, and fungal diversity of dairy cows in response to ingestion of lauric or myristic acid. J Anim Sci 2012; 90:4449-57. [PMID: 22952367 DOI: 10.2527/jas.2011-4624] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The objective of this experiment, part of a larger study, was to investigate changes in rumen bacterial, archaeal, and fungal diversity in cows fed medium-chain saturated fatty acids. In the main study, 6 lactating dairy cows were dosed intraruminally with 240 g/(cow · d) of stearic (SA, control), lauric (LA), or myristic (MA) acid in a replicated 3 × 3 Latin square design trial. Experimental periods were 28 d, and cows were transfaunated between periods. Lauric acid decreased protozoal counts in the rumen by 96% compared with SA and MA (compared with SA, MA had no effect on ruminal protozoa). Whole ruminal contents samples were collected 2, 4, 6, 8, 10, 14, 18, and 24 h after the morning feeding on d 23 of each experimental period, stored frozen, and later composited by cow and period for microbial profile analyses, which involved tag-encoded flexible (FLX) amplicon pyrosequencing to provide diversity analyses of gastrointestinal bacterial, archaeal, and fungal populations of the cattle. The LA treatment, either directly or through its effect on protozoa, had a profound effect on the microbial ecology of the rumen. Ruminal populations of Prevotella, Bacteroides, and Enterorhabdus were decreased (P = 0.04 to P < 0.001) by more than 2-fold in LA treatments compared with SA, and Clostridium populations were decreased (P = 0.01) in LA- compared with MA-treated cows. The proportion of Ruminococcus was not affected by treatment, although the LA treatment had the least proportion of Ruminococcus. Proportions of Eubacterium, Butyrivibrio, Olsenella, and Lactobacillus genera were increased (P = 0.03 to 0.01) by LA compared with MA or SA. The LA treatment, possibly through its effect on protozoa physically associated with archaea, resulted in an increase (P = 0.01) in the archaeal methanogenic genus Methanosphaera and a decrease (P = 0.01) in Methanobrevibacter. Few changes in fungal populations caused by treatment were detected. Collectively, results indicate that LA, either through antiprotozoal or direct antimicrobial effects, altered bacterial and archaeal populations in the rumen of dairy cows, but effects on fungal populations were not clear.
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Affiliation(s)
- A N Hristov
- Department of Dairy and Animal Science, Pennsylvania State University, University Park 16802, USA.
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Yang Q, Wang J, Wang H, Chen X, Ren S, Li X, Xu Y, Zhang H, Li X. Evolution of the microbial community in a full-scale printing and dyeing wastewater treatment system. BIORESOURCE TECHNOLOGY 2012; 117:155-163. [PMID: 22613891 DOI: 10.1016/j.biortech.2012.04.059] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Revised: 04/14/2012] [Accepted: 04/19/2012] [Indexed: 06/01/2023]
Abstract
In this study, the dynamics of bacterial, fungal and archaeal populations in two-stage biological processes of a full-scale printing and dyeing wastewater treatment system were traced using cultivation and molecular biological techniques. The enumeration results indicated that bacteria were the dominant population in the system, in which the ratio of fungi to bacteria decreased in all the treatment units, while the ratio of archaea to bacteria increased significantly, especially in samples from the second-stage biological treatment process. PCR-denaturing gradient gel electrophoresis (DGGE) analysis showed that the microbial diversity increased with system running and 64.6% of bacterial, 57.6% of fungal and 38.2% of archaeal populations remained in the system from the seed sludge during system start-up. In spite of variation in the microbial community and composition of the influents, some bacterial species such as Thauera sp. and Xanthomonadaceae were present simultaneously in all the collected samples.
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Affiliation(s)
- Qingxiang Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China.
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Kumar S, Dagar SS, Sirohi SK, Upadhyay RC, Puniya AK. Microbial profiles, in vitro gas production and dry matter digestibility based on various ratios of roughage to concentrate. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-012-0501-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Sirohi SK, Singh N, Dagar SS, Puniya AK. Molecular tools for deciphering the microbial community structure and diversity in rumen ecosystem. Appl Microbiol Biotechnol 2012; 95:1135-54. [PMID: 22782251 DOI: 10.1007/s00253-012-4262-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 06/20/2012] [Accepted: 06/22/2012] [Indexed: 12/30/2022]
Abstract
Rumen microbial community comprising of bacteria, archaea, fungi, and protozoa is characterized not only by the high population density but also by the remarkable diversity and the most complex microecological interactions existing in the biological world. This unprecedented biodiversity is quite far from full elucidation as only about 15-20 % of the rumen microbes are identified and characterized till date using conventional culturing and microscopy. However, the last two decades have witnessed a paradigm shift from cumbersome and time-consuming classical methods to nucleic acid-based molecular approaches for deciphering the rumen microbial community. These techniques are rapid, reproducible and allow both the qualitative and quantitative assessment of microbial diversity. This review describes the different molecular methods and their applications in elucidating the rumen microbial community.
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Affiliation(s)
- Sunil Kumar Sirohi
- Nutrition Biotechnology Laboratory, Dairy Cattle Nutrition Division, National Dairy Research Institute, Karnal, 132001, Haryana, India.
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Tymensen LD, Beauchemin KA, McAllister TA. Structures of free-living and protozoa-associated methanogen communities in the bovine rumen differ according to comparative analysis of 16S rRNA and mcrA genes. Microbiology (Reading) 2012; 158:1808-1817. [DOI: 10.1099/mic.0.057984-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Lisa D. Tymensen
- Agriculture and Agri-Food Canada, Lethbridge, AB TIJ 4B1, Canada
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46
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OZUTSUMI Y, TAJIMA K, TAKENAKA A, ITABASHI H. ThemcrA gene and 16S rRNA gene in the phylogenetic analysis of methanogens in the rumen of faunated and unfaunated cattle. Anim Sci J 2012; 83:727-34. [DOI: 10.1111/j.1740-0929.2012.01023.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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47
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Diversity and abundance of the rumen and fecal methanogens in Altay sheep native to Xinjiang and the influence of diversity on methane emissions. Arch Microbiol 2011; 194:353-61. [PMID: 22038025 DOI: 10.1007/s00203-011-0757-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 09/09/2011] [Accepted: 09/13/2011] [Indexed: 10/15/2022]
Abstract
This study aims to investigate the influence of diet roughage proportion on the methanogenic communities from the rumen and fecal samples in Altay local sheep native to Xinjiang and better understand the association of methanogenic diversity or abundance with methane emissions of the ruminants. In this study, the high roughage diet was found to cause more methane emissions for either maintenance or ad-lib group, but the total methanogenic abundance was not influenced by roughage proportion and showed no significant difference between groups. Furthermore, the denaturing gradient gel electrophoresis was conducted to reveal the difference in methanogenic diversity. Phylogenetic analysis showed that the sequences obtained were divided into three groups, affiliated to the genus of Methanobrevibacter, Methanocorpusculum and an unidentified methanogenic-like group. Of these sequences, the predominant diversity from the genus of Methanobrevibacter and the unidentified methanogenic-like archaeons in the rumen was found to be significantly induced by the high roughage diet, implying that the variation of diversity at the species or strain level might have an effect on methane emissions from the rumen. Further analysis showed that five methangenic sequences from the rumen were possibly associated with the differential methane emissions.
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Hook SE, Steele MA, Northwood KS, Wright ADG, McBride BW. Impact of high-concentrate feeding and low ruminal pH on methanogens and protozoa in the rumen of dairy cows. MICROBIAL ECOLOGY 2011; 62:94-105. [PMID: 21625972 DOI: 10.1007/s00248-011-9881-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 05/12/2011] [Indexed: 05/30/2023]
Abstract
Non-lactating dairy cattle were transitioned to a high-concentrate diet to investigate the effect of ruminal pH suppression, commonly found in dairy cattle, on the density, diversity, and community structure of rumen methanogens, as well as the density of rumen protozoa. Four ruminally cannulated cows were fed a hay diet and transitioned to a 65% grain and 35% hay diet. The cattle were maintained on an high-concentrate diet for 3 weeks before the transition back to an hay diet, which was fed for an additional 3 weeks. Rumen fluid and solids and fecal samples were obtained prior to feeding during weeks 0 (hay), 1, and 3 (high-concentrate), and 4 and 6 (hay). Subacute ruminal acidosis was induced during week 1. During week 3 of the experiment, there was a significant increase in the number of protozoa present in the rumen fluid (P=0.049) and rumen solids (P=0.004), and a significant reduction in protozoa in the rumen fluid in week 6 (P=0.003). No significant effect of diet on density of rumen methanogens was found in any samples, as determined by real-time PCR. Clone libraries were constructed for weeks 0, 3, and 6, and the methanogen diversity of week 3 was found to differ from week 6. Week 3 was also found to have a significantly altered methanogen community structure, compared to the other weeks. Twenty-two unique 16S rRNA phylotypes were identified, three of which were found only during high-concentrate feeding, three were found during both phases of hay feeding, and seven were found in all three clone libraries. The genus Methanobrevibacter comprised 99% of the clones present. The rumen fluid at weeks 0, 3, and 6 of all the animals was found to contain a type A protozoal population. Ultimately, high-concentrate feeding did not significantly affect the density of rumen methanogens, but did alter methanogen diversity and community structure, as well as protozoal density within the rumen of nonlactating dairy cattle. Therefore, it may be necessary to monitor the rumen methanogen and protozoal communities of dairy cattle susceptible to depressed pH when methane abatement strategies are being investigated.
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Affiliation(s)
- Sarah E Hook
- Department of Animal and Poultry Science, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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Zhou M, McAllister T, Guan L. Molecular identification of rumen methanogens: Technologies, advances and prospects. Anim Feed Sci Technol 2011. [DOI: 10.1016/j.anifeedsci.2011.04.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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50
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Mosoni P, Martin C, Forano E, Morgavi DP. Long-term defaunation increases the abundance of cellulolytic ruminococci and methanogens but does not affect the bacterial and methanogen diversity in the rumen of sheep1. J Anim Sci 2011; 89:783-91. [DOI: 10.2527/jas.2010-2947] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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