1
|
Hackmann TJ, Zhang B. The phenotype and genotype of fermentative prokaryotes. SCIENCE ADVANCES 2023; 9:eadg8687. [PMID: 37756392 PMCID: PMC10530074 DOI: 10.1126/sciadv.adg8687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023]
Abstract
Fermentation is a type of metabolism pervasive in oxygen-deprived environments. Despite its importance, we know little about the range and traits of organisms that carry out this metabolism. Our study addresses this gap with a comprehensive analysis of the phenotype and genotype of fermentative prokaryotes. We assembled a dataset with phenotypic records of 8350 organisms plus 4355 genomes and 13.6 million genes. Our analysis reveals fermentation is both widespread (in ~30% of prokaryotes) and complex (forming ~300 combinations of metabolites). Furthermore, it points to previously uncharacterized proteins involved in this metabolism. Previous studies suggest that metabolic pathways for fermentation are well understood, but metabolic models built in our study show gaps in our knowledge. This study demonstrates the complexity of fermentation while showing that there is still much to learn about this metabolism. All resources in our study can be explored by the scientific community with an online, interactive tool.
Collapse
Affiliation(s)
| | - Bo Zhang
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA
| |
Collapse
|
2
|
Liang J, Ali S, Lv C, Yang H, Zhao X, Ni X, Li C, Danzeng B, Wang Y, Quan G. Dietary protein levels modulate the gut microbiome composition through fecal samples derived from lactating ewes. Front Endocrinol (Lausanne) 2023; 14:1194425. [PMID: 37621652 PMCID: PMC10446493 DOI: 10.3389/fendo.2023.1194425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/02/2023] [Indexed: 08/26/2023] Open
Abstract
In ruminants, the digestion and utilization of dietary proteins are closely linked to the bacterial populations that are present in the gastrointestinal tract. In the present study, 16S rDNA sequencing, together with a metagenomic strategy was used to characterize the fecal bacteria of ewes in the early lactation stage after feeding with three levels of dietary proteins 8.58%, 10.34%, and 13.93%, in three different groups (H_1), (H_m) and (H_h), respectively. A total of 376,278,516 clean data-points were obtained by metagenomic sequencing. Firmicutes and Bacteroidetes were the dominant phyla, regardless of the dietary protein levels. In the H_h group, the phyla Proteobacteria, Caldiserica, and Candidatus_Cryosericota were less abundant than those in the H_I group. In contrast, Lentisphaerae, Chlamydiae, and Planctomycetes were significantly more abundant in the H_h group. Some genera, such as Prevotella, Roseburia, and Firmicutes_unclassified, were less abundant in the H_h group than those in the H_I group. In contrast, Ruminococcus, Ruminococcaceae_noname, Anaerotruncus, Thermotalae, Lentisphaerae_noname, and Paraprevotella were enriched in the H_h group. The acquired microbial genes were mainly clustered into biological processes; molecular functions; cytosol; cellular components; cytoplasm; structural constituents of ribosomes; plasma membranes; translation; and catalytic activities. 205987 genes were significantly enriched in the H_h group. In contrast, 108129 genes were more abundant in the H_I group. Our findings reveal that dynamic changes in fecal bacteria and their genes are strongly influenced by the levels of dietary proteins. We discovered that differentially expressed genes mainly regulate metabolic activity and KEGG demonstrated the primary involvement of these genes in the metabolism of carbohydrates, amino acids, nucleotides, and vitamins. Additionally, genes responsible for metabolism were more abundant in the H_h group. Investigating fecal bacterial characteristics may help researchers develop a dietary formula for lactating ewes to optimize the growth and health of ewes and lambs.
Collapse
Affiliation(s)
- Jiachong Liang
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| | - Sikandar Ali
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
- Zhejiang Vegamax Biotechnology Co., Ltd, Hangzhou, Zhejiang, China
| | - Chunrong Lv
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| | - Hongyuan Yang
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| | - Xiaoqi Zhao
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| | - Xiaojun Ni
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| | - Chunyan Li
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| | - Baiji Danzeng
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| | - Yajing Wang
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Guobo Quan
- The Small Ruminant Department, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan, China
| |
Collapse
|
3
|
Fakih I, Got J, Robles-Rodriguez CE, Siegel A, Forano E, Muñoz-Tamayo R. Dynamic genome-based metabolic modeling of the predominant cellulolytic rumen bacterium Fibrobacter succinogenes S85. mSystems 2023; 8:e0102722. [PMID: 37289026 PMCID: PMC10308913 DOI: 10.1128/msystems.01027-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/14/2023] [Indexed: 06/09/2023] Open
Abstract
Fibrobacter succinogenes is a cellulolytic bacterium that plays an essential role in the degradation of plant fibers in the rumen ecosystem. It converts cellulose polymers into intracellular glycogen and the fermentation metabolites succinate, acetate, and formate. We developed dynamic models of F. succinogenes S85 metabolism on glucose, cellobiose, and cellulose on the basis of a network reconstruction done with the automatic reconstruction of metabolic model workspace. The reconstruction was based on genome annotation, five template-based orthology methods, gap filling, and manual curation. The metabolic network of F. succinogenes S85 comprises 1,565 reactions with 77% linked to 1,317 genes, 1,586 unique metabolites, and 931 pathways. The network was reduced using the NetRed algorithm and analyzed for the computation of elementary flux modes. A yield analysis was further performed to select a minimal set of macroscopic reactions for each substrate. The accuracy of the models was acceptable in simulating F. succinogenes carbohydrate metabolism with an average coefficient of variation of the root mean squared error of 19%. The resulting models are useful resources for investigating the metabolic capabilities of F. succinogenes S85, including the dynamics of metabolite production. Such an approach is a key step toward the integration of omics microbial information into predictive models of rumen metabolism. IMPORTANCE F. succinogenes S85 is a cellulose-degrading and succinate-producing bacterium. Such functions are central for the rumen ecosystem and are of special interest for several industrial applications. This work illustrates how information of the genome of F. succinogenes can be translated to develop predictive dynamic models of rumen fermentation processes. We expect this approach can be applied to other rumen microbes for producing a model of rumen microbiome that can be used for studying microbial manipulation strategies aimed at enhancing feed utilization and mitigating enteric emissions.
Collapse
Affiliation(s)
- Ibrahim Fakih
- Université Clermont Auvergne, INRAE, UMR454 Microbiologie Environnement Digestif et Santé, 63000 Clermont-Ferrand, France
- Université Paris-Saclay, INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, 91120 Palaiseau, France
| | - Jeanne Got
- Université Rennes, Inria, CNRS, IRISA, Dyliss team, 35042 Rennes, France
| | | | - Anne Siegel
- Université Rennes, Inria, CNRS, IRISA, Dyliss team, 35042 Rennes, France
| | - Evelyne Forano
- Université Clermont Auvergne, INRAE, UMR454 Microbiologie Environnement Digestif et Santé, 63000 Clermont-Ferrand, France
| | - Rafael Muñoz-Tamayo
- Université Paris-Saclay, INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, 91120 Palaiseau, France
| |
Collapse
|
4
|
Kamada S, Wakabayashi R, Naganuma T. Phylogenetic Revisit to a Review on Predatory Bacteria. Microorganisms 2023; 11:1673. [PMID: 37512846 PMCID: PMC10385382 DOI: 10.3390/microorganisms11071673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Predatory bacteria, along with the biology of their predatory behavior, have attracted interest in terms of their ecological significance and industrial applications, a trend that has been even more pronounced since the comprehensive review in 2016. This mini-review does not cover research trends, such as the role of outer membrane vesicles in myxobacterial predation, but provides an overview of the classification and newly described taxa of predatory bacteria since 2016, particularly with regard to phylogenetic aspects. Among them, it is noteworthy that in 2020 there was a major phylogenetic reorganization that the taxa hosting Bdellovibrio and Myxococcus, formerly classified as Deltaproteobacteria, were proposed as the new phyla Bdellovibrionota and Myxococcota, respectively. Predatory bacteria have been reported from other phyla, especially from the candidate divisions. Predatory bacteria that prey on cyanobacteria and predatory cyanobacteria that prey on Chlorella have also been found. These are also covered in this mini-review, and trans-phylum phylogenetic trees are presented.
Collapse
Affiliation(s)
- Saki Kamada
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
| | - Ryoka Wakabayashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
| | - Takeshi Naganuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
| |
Collapse
|
5
|
Cleary DFR, Oliveira V, Gomes NCM, Bialecki A, de Voogd NJ. A comparison of free-living and sponge-associated bacterial communities from a remote oceanic island with a focus on calcareous sponges. FEMS Microbiol Ecol 2023; 99:7033423. [PMID: 36758964 PMCID: PMC10022632 DOI: 10.1093/femsec/fiad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/16/2023] [Accepted: 02/08/2023] [Indexed: 02/11/2023] Open
Abstract
Calcareous sponges are an often overlooked element of sponge communities. In contrast to most other sponges, calcareous sponges produce calcium carbonate spicules, as opposed to the siliceous spicules of most sponges. Here, we investigated the bacterial communities of 17 sponge species, including type and paratype specimens of recently described calcareous species, sampled off the remote island of Rodrigues, in the Indian Ocean. The main axis of variation in a PCO analysis of all samples separated noncalcareous sponge species, including Axinyssa aplysinoides, Cinachyrella aff. australiensis, Petrosia seychellensis, Ircinia aff. variabilis, Spongia ceylonensis, Plakinastrella aff. clipptertonensis, Agelas aff. ceylonica, Agelas aff. mauritiana, and Hyrtios erectus from calcareous sponges, the noncalcareous Biemna tubulata, sediment, and seawater. Overall, the bacterial communities of calcareous sponges revealed unique prokaryotic profiles with low abundances of several bacterial phyla, and relatively high abundances of other taxa, for example, the phyla Fibrobacterota, Proteobacteria, and the SAR324 clade, the class Alphaproteobacteria, and orders Cytophagales and Cyanobacteriales, although there was considerable variation among species. Calcareous sponges also had a high dominance of unknown bacterial operational taxonomic units (OTUs). Considering the unique nature of these communities, further studies are needed to better understand the environmental and ecological drivers of calcareous sponge-associated bacterial communities and their relevance as potential sources of novel microbes of biotechnological interest.
Collapse
Affiliation(s)
- D F R Cleary
- Corresponding author. Institute of Environmental Sciences, CML, Leiden University Einsteinweg 2, 2333 CC Leiden, The Netherlands. E-mail:
| | - V Oliveira
- Department of Biology and CESAM, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - N C M Gomes
- Department of Biology and CESAM, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - A Bialecki
- Laboratoire de Chimie et de Biotechnologie des Produits Naturels, Faculté des Sciences et Technologies, Université de La Réunion, 15 Avenue René Cassin, CS 92003, CEDEX 09, 97744 Saint-Denis, France
| | | |
Collapse
|
6
|
Takizawa S, Asano R, Abe K, Fukuda Y, Baba Y, Sakurai R, Tada C, Nakai Y. Relationship Between Rumen Microbial Composition and Fibrolytic Isozyme Activity During the Biodegradation of Rice Straw Powder Using Rumen Fluid. Microbes Environ 2023; 38:ME23041. [PMID: 37766554 PMCID: PMC10522846 DOI: 10.1264/jsme2.me23041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/20/2023] [Indexed: 09/29/2023] Open
Abstract
Rumen fibrolytic microorganisms have been used to increase the rate of lignocellulosic biomass biodegradation; however, the microbial and isozymatic characteristics of biodegradation remain unclear. Therefore, the present study investigated the relationship between rumen microorganisms and fibrolytic isozymes associated with lignocellulosic biomass hydrolysis. Rice straw, a widely available agricultural byproduct, was ground and used as a substrate. The biodegradation of rice straw powder was performed anaerobically in rumen fluid for 48 h. The results obtained revealed that 31.6 and 23.3% of cellulose and hemicellulose, respectively, were degraded. The total concentration of volatile fatty acids showed a 1.8-fold increase (from 85.4 to 151.6 mM) in 48 h, and 1,230.1 mL L-1 of CO2 and 523.5 mL L-1 of CH4 were produced. The major isozymes identified by zymograms during the first 12 h were 51- and 140-kDa carboxymethyl cellulases (CMCases) and 23- and 57-kDa xylanases. The band densities of 37-, 53-, and 58-kDa CMCases and 38-, 44-, and 130-kDa xylanases increased from 24 to 36 h. A microbial ana-lysis indicated that the relative abundances of Prevotella, Fibrobacter, and Bacteroidales RF16 bacteria, Neocallimastix and Cyllamyces fungi, and Dasytricha and Polyplastron protozoa were related to fibrolytic isozyme activity. The present results provide novel insights into the relationships between fibrolytic isozymes and rumen microorganisms during lignocellulose biodegradation.
Collapse
Affiliation(s)
- Shuhei Takizawa
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Yomogida 232–3, Naruko-onsen, Osaki, Miyagi 989–6711, Japan
- Research Fellow of Japan Society for the Promotion of Science, Japan Society for the Promotion of Science, 5–3–1 Kojimachi, Chiyoda-ku, Tokyo 102–0083, Japan
| | - Ryoki Asano
- Department of Agro-Food Science, Faculty of Agro-Food Science, Niigata Agro-Food University, Hiranedai 2416, Tainai, Niigata 959–2702, Japan
| | - Kenichi Abe
- Department of Agro-Food Science, Faculty of Agro-Food Science, Niigata Agro-Food University, Hiranedai 2416, Tainai, Niigata 959–2702, Japan
| | - Yasuhiro Fukuda
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Yomogida 232–3, Naruko-onsen, Osaki, Miyagi 989–6711, Japan
| | - Yasunori Baba
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Suematsu 1–308, Nonoichi, Ishikawa 921–8836, Japan
| | - Riku Sakurai
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Yomogida 232–3, Naruko-onsen, Osaki, Miyagi 989–6711, Japan
| | - Chika Tada
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Yomogida 232–3, Naruko-onsen, Osaki, Miyagi 989–6711, Japan
| | - Yutaka Nakai
- Department of Agro-Food Science, Faculty of Agro-Food Science, Niigata Agro-Food University, Hiranedai 2416, Tainai, Niigata 959–2702, Japan
| |
Collapse
|
7
|
Yan X, Si H, Zhu Y, Li S, Han Y, Liu H, Du R, Pope PB, Qiu Q, Li Z. Integrated multi-omics of the gastrointestinal microbiome and ruminant host reveals metabolic adaptation underlying early life development. MICROBIOME 2022; 10:222. [PMID: 36503572 PMCID: PMC9743514 DOI: 10.1186/s40168-022-01396-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 10/15/2022] [Indexed: 06/07/2023]
Abstract
BACKGROUND The gastrointestinal tract (GIT) microbiome of ruminants and its metabolic repercussions vastly influence host metabolism and growth. However, a complete understanding of the bidirectional interactions that occur across the host-microbiome axis remains elusive, particularly during the critical development stages at early life. Here, we present an integrative multi-omics approach that simultaneously resolved the taxonomic and functional attributes of microbiota from five GIT regions as well as the metabolic features of the liver, muscle, urine, and serum in sika deer (Cervus nippon) across three key early life stages. RESULTS Within the host, analysis of metabolites over time in serum, urine, and muscle (longissimus lumborum) showed that changes in the fatty acid profile were concurrent with gains in body weight. Additional host transcriptomic and metabolomic analysis revealed that fatty acid β-oxidation and metabolism of tryptophan and branched chain amino acids play important roles in regulating hepatic metabolism. Across the varying regions of the GIT, we demonstrated that a complex and variable community of bacteria, viruses, and archaea colonized the GIT soon after birth, whereas microbial succession was driven by the cooperative networks of hub populations. Furthermore, GIT volatile fatty acid concentrations were marked by increased microbial metabolic pathway abundances linked to mannose (rumen) and amino acids (colon) metabolism. Significant functional shifts were also revealed across varying GIT tissues, which were dominated by host fatty acid metabolism associated with reactive oxygen species in the rumen epithelium, and the intensive immune response in both small and large intestine. Finally, we reveal a possible contributing role of necroptosis and apoptosis in enhancing ileum and colon epithelium development, respectively. CONCLUSIONS Our findings provide a comprehensive view for the involved mechanisms in the context of GIT microbiome and ruminant metabolic growth at early life. Video Abstract.
Collapse
Affiliation(s)
- Xiaoting Yan
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710100, China
| | - Huazhe Si
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Yuhang Zhu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Songze Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Yu Han
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Hanlu Liu
- Department of Special Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Rui Du
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
- Jilin Provincial Engineering Research Center for Efficient Breeding and Product Development of Sika Deer, Changchun, 130118, China
- Key Lab of Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, 130118, China
| | - Phillip B Pope
- Faculty of Biosciences, Norwegian University of Life Sciences, 1433, Ås, Norway.
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1433, Ås, Norway.
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710100, China.
| | - Zhipeng Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China.
- Jilin Provincial Engineering Research Center for Efficient Breeding and Product Development of Sika Deer, Changchun, 130118, China.
- Key Lab of Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China.
| |
Collapse
|
8
|
Jiang Q, Lin L, Xie F, Jin W, Zhu W, Wang M, Qiu Q, Li Z, Liu J, Mao S. Metagenomic insights into the microbe-mediated B and K 2 vitamin biosynthesis in the gastrointestinal microbiome of ruminants. MICROBIOME 2022; 10:109. [PMID: 35864536 PMCID: PMC9306216 DOI: 10.1186/s40168-022-01298-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND B and K2 vitamins, essential nutrients in host metabolism, can be synthesized by the rumen microbiome in ruminants and subsequently absorbed by the host. However, the B and K2 vitamin biosynthesis by the whole gastrointestinal microbiome and their abundances in different dietary strategies are largely unknown. Here, we reanalyzed our previous large-scale metagenomic data on the gastrointestinal microbiome of seven ruminant species and recruited 17,425 nonredundant microbial genomes from published datasets to gain a comprehensive understanding of the microbe-mediated B and K2 vitamin biosynthesis in ruminants. RESULTS We identified 1,135,807 genes and 167 enzymes involved in B and K2 vitamin biosynthesis. Our results indicated that the total abundances of B and K2 vitamin biosynthesis were dominant in the stomach microbiome, while the biosynthesis of thiamine, niacin, and pyridoxine was more abundant in the large intestine. By examining 17,425 nonredundant genomes, we identified 2366 high-quality genomes that were predicted to de novo biosynthesize at least one vitamin. Genomic analysis suggested that only 2.7% of these genomes can synthesize five or more vitamins, and nearly half of genomes can synthesize only one vitamin. Moreover, we found that most genomes possessed cobalamin transporters or cobalamin-dependent enzymes to consume cobalamin directly, and only a few microbial genomes possessed a complete cobalamin biosynthesis pathway. Based on these genomic data, we examined the effect of the high-grain (HG) diet on the vitamin biosynthesis of the rumen microbiome of dairy cattle. We revealed that most vitamin biosynthesis was enhanced in the HG group, while only cobalamin synthesis was inhibited in the HG group, indicating that dietary fiber is vital for cobalamin biosynthesis. CONCLUSIONS We primarily provided a gene catalog and 2366 microbial genomes involved in B and K2 vitamin biosynthesis in ruminants. Our findings demonstrated the regional heterogeneity and dietary effect of vitamin biosynthetic potential in the ruminant gastrointestinal microbiome and interpreted the biosynthesis mechanisms of these microbes and their physiological adaptability. This study expands our understanding of microbe-mediated vitamin biosynthesis in ruminants and may provide novel targets for manipulation to improve the production of these essential vitamins. Video abstract.
Collapse
Affiliation(s)
- Qian Jiang
- Centre for Ruminant Nutrition and Feed Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Limei Lin
- Centre for Ruminant Nutrition and Feed Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Fei Xie
- Centre for Ruminant Nutrition and Feed Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Wei Jin
- Centre for Ruminant Nutrition and Feed Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Weiyun Zhu
- Centre for Ruminant Nutrition and Feed Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Min Wang
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Zhipeng Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Junhua Liu
- Centre for Ruminant Nutrition and Feed Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.
| | - Shengyong Mao
- Centre for Ruminant Nutrition and Feed Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.
| |
Collapse
|
9
|
Zhang Z, Gao X, Dong W, Huang B, Wang Y, Zhu M, Wang C. Plant cell wall breakdown by hindgut microorganisms: can we get scientific insights from rumen microorganisms? J Equine Vet Sci 2022; 115:104027. [PMID: 35661771 DOI: 10.1016/j.jevs.2022.104027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 01/20/2023]
Abstract
Equines and ruminants have evolved as grazing herbivores with specialized gastrointestinal tracts capable of utilizing a wide range of fibrous feeds. In China, agricultural by-products, including corn straw, wheat straw, peanut vine, wheat husk, rice husk, and grass hay, have been extensively included in both equine and ruminant diets. These plant materials, which are composed predominantly of cellulose, hemicellulose, noncellulosic polysaccharides, and lignin, are largely undegradable by equines and ruminants themselves. Their breakdown is accomplished by communities of resident microorganisms that live in symbiotic or mutualistic associations with the host. Information relating to microbial composition in the hindgut and rumen has become increasingly available. Rumen fermentation is unique in that plant cell wall breakdown relies on the cooperation between microorganisms that produce fibrolytic enzymes and that ruminant animals provide an anaerobic fermentation chamber. Similar to the rumen, the equine hindgut is also an immensely enlarged fermentative chamber that includes an extremely abundant and highly complex community of microorganisms. However, few studies have characterized the microbial functions and their utilization process of lignocellulosic feeds within the equine hindgut. The process of understanding and describing plant cell wall degradation mechanisms in the equine hindgut ecosystem is important for providing information for proper feeding practices to be implemented. In the present study, we gather existing information on the rumen and equine ecosystem and provide scientific insights for understanding the process of plant cell wall breakdown within the hindgut.
Collapse
Affiliation(s)
- Zhenwei Zhang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
| | - Xu Gao
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
| | - Wanting Dong
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
| | - Bingjian Huang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
| | - Yonghui Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
| | - Mingxia Zhu
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China.
| |
Collapse
|
10
|
Zepeda B, Verdonk JC. RNA Extraction from Plant Tissue with Homemade Acid Guanidinium Thiocyanate Phenol Chloroform (AGPC). Curr Protoc 2022; 2:e351. [PMID: 35077031 DOI: 10.1002/cpz1.351] [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] [Indexed: 01/03/2023]
Abstract
Gene expression studies are a powerful technique to study biological processes, and isolating RNA that is pure, intact, and in sufficient amounts for downstream applications is key. Over the years, the field has moved to the use of commercial kits and ready-made extraction buffers for RNA isolation. This became particularly problematic during the COVID-19 crisis when supply chains were affected and when RNA extraction and analysis reagents were suddenly scarce at a time when they were particularly required. Acid guanidinium thiocyanate-phenol-chloroform (AGPC) is one of the oldest RNA extraction solutions, in use since 1987. It is known as a ready-made solution, sold under different brand names, and is typically the most expensive reagent in the RNA extraction process. In this article, we describe how to prepare a low-cost homemade AGPC solution and provide tips on how to use it for obtaining high-quality RNA, as well as describe possible modifications for different conditions. The protocol is based on a phase separation, where RNA is maintained in the aqueous phase and DNA and proteins remain in the interphase and organic phase. After cleaning, precipitation, and resuspension steps, the RNA is ready to be quantified and used for downstream applications. By following this protocol, good yields of high-quality RNA can be obtained from a wide variety of tissues and organisms, and we exemplify the approach here using plant tissues. Some plant tissues contain extra interferents (such as sugars), and for high-quality RNA isolation from those tissues, an alternate protocol is provided. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: RNA isolation with homemade acid guanidinium thiocyanate-phenol-chloroform (AGPC) Alternate Protocol: RNA isolation from high carbohydrate-containing tissues using an NTES-AGPC combination.
Collapse
Affiliation(s)
- Baltasar Zepeda
- Horticulture and Product Physiology, Plant Science Group, Wageningen University, Wageningen, The Netherlands
| | - Julian C Verdonk
- Horticulture and Product Physiology, Plant Science Group, Wageningen University, Wageningen, The Netherlands
| |
Collapse
|
11
|
Takizawa S, Asano R, Fukuda Y, Baba Y, Tada C, Nakai Y. Shifts in xylanases and the microbial community associated with xylan biodegradation during treatment with rumen fluid. Microb Biotechnol 2021; 15:1729-1743. [PMID: 34964273 PMCID: PMC9151333 DOI: 10.1111/1751-7915.13988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 11/03/2021] [Accepted: 11/24/2021] [Indexed: 11/29/2022] Open
Abstract
Treatment with rumen fluid improves methane production from non‐degradable lignocellulosic biomass during subsequent methane fermentation; however, the kinetics of xylanases during treatment with rumen fluid remain unclear. This study aimed to identify key xylanases contributing to xylan degradation and their individual activities during xylan treatment with bovine rumen microorganisms. Xylan was treated with bovine rumen fluid at 37°C for 48 h under anaerobic conditions. Total solids were degraded into volatile fatty acids and gases during the first 24 h. Zymography showed that xylanases of 24, 34, 85, 180, and 200 kDa were highly active during the first 24 h. Therefore, these xylanases are considered to be crucial for xylan degradation during treatment with rumen fluid. Metagenomic analysis revealed that the rumen microbial community’s structure and metabolic function temporally shifted during xylan biodegradation. Although statistical analyses did not reveal significantly positive correlations between xylanase activities and known xylanolytic bacterial genera, they positively correlated with protozoal (e.g., Entodinium, Diploplastron, and Eudiplodinium) and fungal (e.g., Neocallimastix, Orpinomyces, and Olpidium) genera and unclassified bacteria. Our findings suggest that rumen protozoa, fungi, and unclassified bacteria are associated with key xylanase activities, accelerating xylan biodegradation into volatile fatty acids and gases, during treatment of lignocellulosic biomass with rumen fluid.
Collapse
Affiliation(s)
- Shuhei Takizawa
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Japan.,Japan Society for the Promotion of Science, Chiyoda-ku, Japan
| | - Ryoki Asano
- Department of Agro-Food Science, Faculty of Agro-Food Science, Niigata Agro-Food University, Tainai, Japan
| | - Yasuhiro Fukuda
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Japan
| | - Yasunori Baba
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Japan
| | - Chika Tada
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Japan
| | - Yutaka Nakai
- Department of Agro-Food Science, Faculty of Agro-Food Science, Niigata Agro-Food University, Tainai, Japan
| |
Collapse
|
12
|
Effects of Partially Hydrolyzed Guar Gum Supplementation on the Fecal Microbiotas of Piglets. Pathogens 2021; 10:pathogens10111420. [PMID: 34832576 PMCID: PMC8619618 DOI: 10.3390/pathogens10111420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
Probiotics and prebiotics have become viable alternatives of growth-promoting antimicrobials in animal production. Here, we tested partially hydrolyzed guar gum (PHGG) as a possible prebiotic for piglets in the commercial farm. Five hundred and ninety-four piglets were used for the experiments, with 293 given a normal pig feed (control), while the rest the feed plus 0.06% (w/w) of PHGG (PHGG). One and three months post-PHGG supplementation, fecal samples were collected from randomly selected 20 piglets in each group and analyzed for microbiota and organic acid concentrations. Notably, the abundance of Streptococcus, and unclassified Ruminococcaceae were lower (p < 0.05) in PHGG than in control, one-month post-supplementation. Lactobacillus and Prevotella were higher (p < 0.05), while Streptococcus was lower (p < 0.05), in PHGG than in control, three months post-supplementation. The concentrations of acetate, propionate, and butyrate were greater in PHGG than in control, three months post-supplementation. Finally, PHGG grew faster and had fewer deaths until slaughter time (p < 0.05), than control. We concluded that PHGG not only was an effective prebiotic to alter gut microbiota of weanling piglets but also can possibly promote body weight accretion and health.
Collapse
|
13
|
Takizawa S, Asano R, Fukuda Y, Baba Y, Tada C, Nakai Y. Characteristics of various fibrolytic isozyme activities in the rumen microbial communities of Japanese Black and Holstein Friesian cattle under different conditions. Anim Sci J 2021; 92:e13653. [PMID: 34714591 PMCID: PMC9286360 DOI: 10.1111/asj.13653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/13/2021] [Accepted: 09/28/2021] [Indexed: 11/30/2022]
Abstract
Rumen microorganisms produce various fibrolytic enzymes and degrade lignocellulosic materials into nutrient sources for ruminants; therefore, the characterization of fibrolytic enzymes contributing to the polysaccharide degradation in the rumen microbiota is important for efficient animal production. This study characterized the fibrolytic isozyme activities of a rumen microbiota from four groups of housed cattle (1, breeding Japanese Black; 2, feedlot Japanese Black; 3, lactating Holstein Friesian; 4, dry Holstein Friesian). Rumen fluids in all cattle groups showed similar concentrations of total volatile fatty acids and reducing sugars, whereas acetic acid contents and pH were different among them. Predominant genera were commonly detected in all cattle, although the bacterial compositions were different among cattle groups. Zymograms of whole proteins in rumen fluids showed endoglucanase activities at 55 and 57 kDa and xylanase activity at 44 kDa in all cattle. Meanwhile, several fibrolytic isozyme activities differed among cattle groups and individuals. Treponema, Succinivibrio, Anaeroplasma, Succiniclasticum, Ruminococcus, and Butyrivibrio showed positive correlations with fibrolytic isozyme activities. Further, endoglucanase activity at 68 kDa was positively correlated with pH. This study suggests the characteristics of fibrolytic isozyme activities and their correlations with the rumen microbiota.
Collapse
Affiliation(s)
- Shuhei Takizawa
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Japan.,Research Fellow of Japan Society for the Promotion of Science, Japan Society for the Promotion of Science, Chiyoda-ku, Japan
| | - Ryoki Asano
- Department of Agro-Food Science, Faculty of Agro-Food Science, Niigata Agro-Food University, Tainai, Japan
| | - Yasuhiro Fukuda
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Japan
| | - Yasunori Baba
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Japan
| | - Chika Tada
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Japan
| | - Yutaka Nakai
- Department of Agro-Food Science, Faculty of Agro-Food Science, Niigata Agro-Food University, Tainai, Japan
| |
Collapse
|
14
|
Pi Y, Hu J, Bai Y, Wang Z, Wu Y, Ye H, Zhang S, Tao S, Xiao Y, Han D, Ni D, Zou X, Wang J. Effects of dietary fibers with different physicochemical properties on fermentation kinetics and microbial composition by fecal inoculum from lactating sows in vitro. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:907-917. [PMID: 32737882 DOI: 10.1002/jsfa.10698] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/22/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Efficient utilization of dietary fibers (DFs) is important for optimizing feed resource utilization and animal health. The aim of the current study was to assess the effects of DFs with varying physicochemical properties (bulky, viscous, and fermentable) on fermentation kinetics and microbial composition during in vitro fermentation by fecal inoculum from lactating sow. According to the physicochemical properties, three different DFs, lignocellulose (LC), modified cassava starch (MCS) and konjac flour (KF) were selected as bulky fiber, fermentable fiber and viscous fiber respectively. Gas production, short-chain fatty acids (SCFAs) profiles and microbial composition were monitored during the fermentation. RESULTS Results showed that the gas production in 72 h (GP72h ) ranked as: KF > MCS > LC (P < 0.05). The halftime of asymptotic gas production ranked as: KF < MCS = LC (P < 0.001). At 36 h of fermentation, MCS group showed higher concentrations of formic acid and lactate than LC and KF groups, whereas KF group showed higher concentrations of propionate and butyrate than LC and MCS groups (P < 0.05). At 72 h of fermentation, KF group showed higher concentrations of formic acid, lactate and propionate than LC and MCS groups, whereas MCS group showed higher concentrations of acetate and butyrate than LC and KF groups (P < 0.05). At 36 h of fermentation, Anaerovibrio and Erysipelatoclostridium abundances were higher in KF group, whereas Proteiniclasticum abundance was higher in MCS group. At 72 h of fermentation, the abundance of Fibrobacter in LC group was higher than that in MCS and KF groups. In addition, we also observed that the abundances of certain specific bacteria (Anaerovibrio and Erysipelatoclostridium) were closely related to the SCFAs production (propionate and butyrate) at different fermentation times. CONCLUSION Collectively, the present study revealed that KF is a fast fermentation fiber which could produce propionate and butyrate rapidly, whereas LC is difficult to be fermented by bacteria. In addition, the fermentation of DFs with different physicochemical properties had divergent impacts on microbial composition and SCFA production. These findings deepen our understanding of the mechanisms of interaction between DFs and intestinal microbiota, and provide new ideas for the rational use of fiber resources in lactating sows. © 2020 Society of Chemical Industry.
Collapse
Affiliation(s)
- Yu Pi
- State Key Laboratory of Biological Feed, Ministry of Agriculture and Rural Affairs, Boen Biotechnology Co. Ltd, Ganzhou, China
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jie Hu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yu Bai
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhibo Wang
- State Key Laboratory of Biological Feed, Ministry of Agriculture and Rural Affairs, Boen Biotechnology Co. Ltd, Ganzhou, China
| | - Yujun Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hao Ye
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shiyi Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shiyu Tao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yingping Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Quality and Standard for Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Dandan Han
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Dongjiao Ni
- State Key Laboratory of Biological Feed, Ministry of Agriculture and Rural Affairs, Boen Biotechnology Co. Ltd, Ganzhou, China
| | - Xinhua Zou
- State Key Laboratory of Biological Feed, Ministry of Agriculture and Rural Affairs, Boen Biotechnology Co. Ltd, Ganzhou, China
| | - Junjun Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| |
Collapse
|
15
|
Honan M, Feng X, Tricarico J, Kebreab E. Feed additives as a strategic approach to reduce enteric methane production in cattle: modes of action, effectiveness and safety. ANIMAL PRODUCTION SCIENCE 2021. [DOI: 10.1071/an20295] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
16
|
Exploration of the effects of altitude change on bacteria and fungi in the rumen of yak (Bos grunniens). Arch Microbiol 2020; 203:835-846. [PMID: 33070234 DOI: 10.1007/s00203-020-02072-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/18/2020] [Accepted: 10/01/2020] [Indexed: 12/14/2022]
Abstract
The yak (Bos grunniens) is a ruminant animal with strong regional adaptability. However, little is known about the adaptation of the rumen microbial community of yaks at different altitudes and the adaptation mechanism of the host and intestinal microorganisms to the habitat. We investigated the adaptability of the rumen microorganisms of yaks at high and low altitudes. We also compared and analyzed the abundance and diversity of core microorganisms and those that varied between different animals. The aim was to compare the rumen bacterial and fungal communities of grazing yak living at two elevations. Bacteroidetes, Firmicutes, Ascomycota, and Chytridiomycota were the dominant bacteria in the plateau and low-altitude regions. Significant differences between the dominant microorganisms in the rumen of yaks were evident in the two regions. The proportion of fiber-degrading bacteria was significantly different between yaks dwelling at high-altitude and low-altitude regions. The abundance of starch-degrading bacteria was not significantly different with altitude. Species clustering similarity analysis showed that the rumen microorganisms in the two areas were obviously isolated and clustered into branches. Functional prediction showed significant differences in rumen microbial methane metabolism, starch and sucrose metabolism, ion-coupled transporter and bacterial secretion system at different altitudes. Overall, the results of this study improved our understanding of the abundance and composition of microorganisms in the rumen of yak at different altitudes.
Collapse
|
17
|
Kobayashi R, Nagaoka K, Nishimura N, Koike S, Takahashi E, Niimi K, Murase H, Kinjo T, Tsukahara T, Inoue R. Comparison of the fecal microbiota of two monogastric herbivorous and five omnivorous mammals. Anim Sci J 2020; 91:e13366. [PMID: 32285557 PMCID: PMC7216987 DOI: 10.1111/asj.13366] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/19/2020] [Accepted: 03/10/2020] [Indexed: 02/06/2023]
Abstract
Fecal microbiota in seven different monogastric animal species, elephant, horse, human, marmoset, mouse, pig and, rat were compared using the same analytical protocol of 16S rRNA metagenome. Fecal microbiota in herbivores showed higher alpha diversity than omnivores except for pigs. Additionally, principal coordinate analysis based on weighted UniFrac distance demonstrated that herbivores and pigs clustered together, whereas other animal species were separately aggregated. In view of butyrate- and lactate-producing bacteria, predominant genera were different depending on animal species. For example, the abundance of Faecalibacterium, a known butyrate producer, was 8.02% ± 3.22% in human while it was less than 1% in other animal species. Additionally, Bifidobacterium was a predominant lactate producer in human and marmoset, while it was rarely detected in other omnivores. The abundance of lactate-producing bacteria in herbivores was notably lower than omnivores. On the other hand, herbivores as well as pig possess Fibrobacter, a cellulolytic bacterium. This study demonstrated that fecal microbiota in herbivorous animals is similar, sharing some common features such as higher alpha diversity and higher abundance of cellulolytic bacterium. On the other hand, omnivorous animals seem to possess unique fecal microbiota. It is of interest that pigs, although omnivore, have fecal microbiota showing some common features with herbivores.
Collapse
Affiliation(s)
- Rana Kobayashi
- Laboratory of Animal Science, Kyoto Prefectural University, Kyoto, Japan
| | - Kentaro Nagaoka
- Laboratory of Veterinary Physiology, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Naomichi Nishimura
- College of Agriculture, Academic Institute, Shizuoka University, Shizuoka, Japan
| | - Satoshi Koike
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Eiki Takahashi
- Research Resources Division, RIKEN Center for Brain Science, Wako, Japan
| | - Kimie Niimi
- Research Resources Division, RIKEN Center for Brain Science, Wako, Japan
| | - Harutaka Murase
- Japan Racing Association, Hidaka Training and Research Center, Urakawa-cho, Japan
| | - Teruo Kinjo
- Okinawa Zoo and Museum, Okinawa Zoo Animal Hospital, Okinawa, Japan
| | | | - Ryo Inoue
- Laboratory of Animal Science, Kyoto Prefectural University, Kyoto, Japan
| |
Collapse
|
18
|
Martínez-Álvaro M, Auffret MD, Stewart RD, Dewhurst RJ, Duthie CA, Rooke JA, Wallace RJ, Shih B, Freeman TC, Watson M, Roehe R. Identification of Complex Rumen Microbiome Interaction Within Diverse Functional Niches as Mechanisms Affecting the Variation of Methane Emissions in Bovine. Front Microbiol 2020; 11:659. [PMID: 32362882 PMCID: PMC7181398 DOI: 10.3389/fmicb.2020.00659] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/23/2020] [Indexed: 11/13/2022] Open
Abstract
A network analysis including relative abundances of all ruminal microbial genera (archaea, bacteria, fungi, and protists) and their genes was performed to improve our understanding of how the interactions within the ruminal microbiome affects methane emissions (CH4). Metagenomics and CH4 data were available from 63 bovines of a two-breed rotational cross, offered two basal diets. Co-abundance network analysis revealed 10 clusters of functional niches. The most abundant hydrogenotrophic Methanobacteriales with key microbial genes involved in methanogenesis occupied a different functional niche (i.e., "methanogenesis" cluster) than methylotrophic Methanomassiliicoccales (Candidatus Methanomethylophylus) and acetogens (Blautia). Fungi and protists clustered together and other plant fiber degraders like Fibrobacter occupied a seperate cluster. A Partial Least Squares analysis approach to predict CH4 variation in each cluster showed the methanogenesis cluster had the best prediction ability (57.3%). However, the most important explanatory variables in this cluster were genes involved in complex carbohydrate degradation, metabolism of sugars and amino acids and Candidatus Azobacteroides carrying nitrogen fixation genes, but not methanogenic archaea and their genes. The cluster containing Fibrobacter, isolated from other microorganisms, was positively associated with CH4 and explained 49.8% of its variability, showing fermentative advantages compared to other bacteria and fungi in providing substrates (e.g., formate) for methanogenesis. In other clusters, genes with enhancing effect on CH4 were related to lactate and butyrate (Butyrivibrio and Pseudobutyrivibrio) production and simple amino acids metabolism. In comparison, ruminal genes negatively related to CH4 were involved in carbohydrate degradation via lactate and succinate and synthesis of more complex amino acids by γ-Proteobacteria. When analyzing low- and high-methane emitters data in separate networks, competition between methanogens in the methanogenesis cluster was uncovered by a broader diversity of methanogens involved in the three methanogenesis pathways and larger interactions within and between communities in low compared to high emitters. Generally, our results suggest that differences in CH4 are mainly explained by other microbial communities and their activities rather than being only methanogens-driven. Our study provides insight into the interactions of the rumen microbial communities and their genes by uncovering functional niches affecting CH4, which will benefit the development of efficient CH4 mitigation strategies.
Collapse
Affiliation(s)
- Marina Martínez-Álvaro
- Scotland’s Rural College, Edinburgh, United Kingdom
- Institute for Animal Science and Technology, Polytechnic University of Valencia, Valencia, Spain
| | | | - Robert D. Stewart
- Edinburgh Genomics, The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
| | | | | | | | - R. John Wallace
- The Rowett Institute, University of Aberdeen, Aberdeen, United Kingdom
| | - Barbara Shih
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
| | - Tom C. Freeman
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
| | - Mick Watson
- Edinburgh Genomics, The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
| | - Rainer Roehe
- Scotland’s Rural College, Edinburgh, United Kingdom
| |
Collapse
|
19
|
Shi F, Guo N, Degen A, Niu J, Wei H, Jing X, Ding L, Shang Z, Long R. Effects of level of feed intake and season on digestibility of dietary components, efficiency of microbial protein synthesis, rumen fermentation and ruminal microbiota in yaks. Anim Feed Sci Technol 2020. [DOI: 10.1016/j.anifeedsci.2019.114359] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
20
|
Chaucheyras-Durand F, Ameilbonne A, Auffret P, Bernard M, Mialon MM, Dunière L, Forano E. Supplementation of live yeast based feed additive in early life promotes rumen microbial colonization and fibrolytic potential in lambs. Sci Rep 2019; 9:19216. [PMID: 31844130 PMCID: PMC6914811 DOI: 10.1038/s41598-019-55825-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 12/03/2019] [Indexed: 02/06/2023] Open
Abstract
Rumen microbiota is of paramount importance for ruminant digestion efficiency as the microbial fermentations supply the host animal with essential sources of energy and nitrogen. Early separation of newborns from the dam and distribution of artificial milk (Artificial Milking System or AMS) could impair rumen microbial colonization, which would not only affect rumen function but also have possible negative effects on hindgut homeostasis, and impact animal health and performance. In this study, we monitored microbial communities in the rumen and the feces of 16 lambs separated from their dams from 12 h of age and artificially fed with milk replacer and starter feed from d8, in absence or presence of a combination of the live yeast Saccharomyces cerevisiae CNCM I-1077 and selected yeast metabolites. Microbial groups and targeted bacterial species were quantified by qPCR and microbial diversity and composition were assessed by 16S rDNA amplicon sequencing in samples collected from birth to 2 months of age. The fibrolytic potential of the rumen microbiota was analyzed with a DNA microarray targeting genes coding for 8 glycoside hydrolase (GH) families. In Control lambs, poor establishment of fibrolytic communities was observed. Microbial composition shifted as the lambs aged. The live yeast supplement induced significant changes in relative abundances of a few bacterial OTUs across time in the rumen samples, among which some involved in crucial rumen function, and favored establishment of Trichostomatia and Neocallimastigaceae eukaryotic families. The supplemented lambs also harbored greater abundances in Fibrobacter succinogenes after weaning. Microarray data indicated that key cellulase and hemicellulase encoding-genes were present from early age in the rumen and that in the Supplemented lambs, a greater proportion of hemicellulase genes was present. Moreover, a higher proportion of GH genes from ciliate protozoa and fungi was found in the rumen of those animals. This yeast combination improved microbial colonization in the maturing rumen, with a potentially more specialized ecosystem towards efficient fiber degradation, which suggests a possible positive impact on lamb gut development and digestive efficiency.
Collapse
Affiliation(s)
- Frédérique Chaucheyras-Durand
- Lallemand SAS, 31702, Blagnac, France. .,Université Clermont Auvergne, INRA, UMR 454 MEDIS, F-63000, Clermont-Ferrand, France.
| | - Aurélie Ameilbonne
- Lallemand SAS, 31702, Blagnac, France.,Université Clermont Auvergne, INRA, UMR 454 MEDIS, F-63000, Clermont-Ferrand, France
| | - Pauline Auffret
- Université Clermont Auvergne, INRA, UMR 454 MEDIS, F-63000, Clermont-Ferrand, France.,Ifremer, UMR, 241 EIO, Tahiti, French Polynesia
| | - Mickaël Bernard
- UE 1414 Herbipôle, INRA Auvergne Rhône Alpes, F-63122, Saint-Genès Champanelle, France
| | - Marie-Madeleine Mialon
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR 1213 Herbivores, F-63000, Clermont-Ferrand, France
| | - Lysiane Dunière
- Lallemand SAS, 31702, Blagnac, France.,Université Clermont Auvergne, INRA, UMR 454 MEDIS, F-63000, Clermont-Ferrand, France
| | - Evelyne Forano
- Université Clermont Auvergne, INRA, UMR 454 MEDIS, F-63000, Clermont-Ferrand, France
| |
Collapse
|
21
|
An expansin-like protein expands forage cell walls and synergistically increases hydrolysis, digestibility and fermentation of livestock feeds by fibrolytic enzymes. PLoS One 2019; 14:e0224381. [PMID: 31689330 PMCID: PMC6830940 DOI: 10.1371/journal.pone.0224381] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 10/12/2019] [Indexed: 11/19/2022] Open
Abstract
Bacterial expansin-like proteins have synergistically increased cellulose hydrolysis by cellulolytic enzymes during the initial stages of biofuel production, but they have not been tested on livestock feeds. The objectives of this study were to: isolate and express an expansin-like protein (BsEXLX1), to verify its disruptive activity (expansion) on cotton fibers by immunodetection (Experiment 1), and to determine the effect of dose, pH and temperature for BsEXLX1 and cellulase to synergistically hydrolyze filter paper (FP) and carboxymethyl cellulose (CMC) under laboratory (Experiment 2) and simulated ruminal (Experiment 3) conditions. In addition, we determined the ability of BsEXLX1 to synergistically increase hydrolysis of corn and bermudagrass silages by an exogenous fibrolytic enzyme (EFE) (Experiment 4) and how different doses of BsEXLX1 and EFE affect the gas production (GP), in vitro digestibility and fermentation of a diet for dairy cows (Experiment 5). In Experiment 1, immunofluorescence-based examination of cotton microfiber treated without or with recombinant expansin-like protein expressed from Bacillus subtilis (BsEXLX1) increased the surface area by > 100% compared to the untreated control. In Experiment 2, adding BsEXLX1 (100 μg/g FP) to cellulase (0.0148 FPU) increased release of reducing sugars compared to cellulase alone by more than 40% (P < 0.01) at optimal pH (4.0) and temperature (50°C) after 24 h. In Experiment 3 and 4, adding BsEXLX1 to cellulase or EFE, synergistically increased release of reducing sugars from FP, corn and bermudagrass silages under simulated ruminal conditions (pH 6.0, 39°C). In Experiment 5, increasing the concentration of BsEXLX1 linearly increased (P < 0.01) GP from fermentation of a diet for dairy cows by up to 17.8%. Synergistic effects between BsEXLX1 and EFE increased in vitro NDF digestibility of the diet by 23.3% compared to the control. In vitro digestibility of hemicellulose and butyrate concentration were linearly increased by BsEXLX1 compared to the control. This study demonstrated that BsEXLX1 can improve the efficacy of cellulase and EFE at hydrolyzing pure substrates and dairy cow feeds, respectively.
Collapse
|
22
|
Ren Z, Yao R, Liu Q, Deng Y, Shen L, Deng H, Zuo Z, Wang Y, Deng J, Cui H, Hu Y, Ma X, Fang J. Effects of antibacterial peptides on rumen fermentation function and rumen microorganisms in goats. PLoS One 2019; 14:e0221815. [PMID: 31469857 PMCID: PMC6716671 DOI: 10.1371/journal.pone.0221815] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 08/15/2019] [Indexed: 01/09/2023] Open
Abstract
Although many studies have confirmed that antimicrobial peptides (AMPs: PBD-mI and LUC-n) can be used as feed additives, there are few reports of their use in ruminants. The present study aimed to investigate the impact of AMPs on ameliorating rumen fermentation function and rumen microorganisms in goats. Eighteen 4-month-old Chuanzhong black goats were used in a 60-day experiment (6 goats per group). Group I was used as the control and was fed a basal diet, the group II were fed the basal diet supplemented with 2 g of AMPs [per goat/day] and group III were fed the basal diet supplemented 3 g of AMPs [per goat/day], respectively. Rumen fluid samples were collected at 0, 20 and 60 days. Bacterial 16S rRNA genes and ciliate protozoal 18S rRNA genes were amplified by PCR from DNA extracted from rumen samples. The amplicons were sequenced by Illumina MiSeq. Rumen fermentation parameters and digestive enzyme activities were also examined. Our results showed that dietary supplementation with AMPs increased the levels of the bacterial genera Fibrobacter, Anaerovibrio and Succiniclasticum and also increased the ciliates genus Ophryoscolex, but reduced the levels of the bacterial genera Selenomonas, Succinivibrio and Treponema, and the ciliate genera Polyplastron, Entodinium, Enoploplastron and Isotricha. Supplementation with AMPs increased the activities of xylanase, pectinase and lipase in the rumen, and also increased the concentrations of acetic acid, propionic acid and total volatile fatty acids. These changes were associated with improved growth performance in the goats. The results revealed that the goats fed AMPs showed improved rumen microbiota structures, altered ruminal fermentation, and improved efficiency regarding the utilization of feed; thereby indicating that AMPs can improve growth performance. AMPs are therefore suitable as feed additives in juvenile goats.
Collapse
Affiliation(s)
- Zhihua Ren
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, Key Laboratory of Environmental Hazard and Animal Disease of Sichuan Province, College of Veterinary Medicine, Sichuang Agricultural University, Chengdu Sichuang, China
| | - Renjie Yao
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, Key Laboratory of Environmental Hazard and Animal Disease of Sichuan Province, College of Veterinary Medicine, Sichuang Agricultural University, Chengdu Sichuang, China
| | - Qi Liu
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, Key Laboratory of Environmental Hazard and Animal Disease of Sichuan Province, College of Veterinary Medicine, Sichuang Agricultural University, Chengdu Sichuang, China
| | - Youtian Deng
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, Key Laboratory of Environmental Hazard and Animal Disease of Sichuan Province, College of Veterinary Medicine, Sichuang Agricultural University, Chengdu Sichuang, China
| | - Liuhong Shen
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, Key Laboratory of Environmental Hazard and Animal Disease of Sichuan Province, College of Veterinary Medicine, Sichuang Agricultural University, Chengdu Sichuang, China
| | - Huidan Deng
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, Key Laboratory of Environmental Hazard and Animal Disease of Sichuan Province, College of Veterinary Medicine, Sichuang Agricultural University, Chengdu Sichuang, China
| | - Zhicai Zuo
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, Key Laboratory of Environmental Hazard and Animal Disease of Sichuan Province, College of Veterinary Medicine, Sichuang Agricultural University, Chengdu Sichuang, China
| | - Ya Wang
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, Key Laboratory of Environmental Hazard and Animal Disease of Sichuan Province, College of Veterinary Medicine, Sichuang Agricultural University, Chengdu Sichuang, China
| | - Junliang Deng
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, Key Laboratory of Environmental Hazard and Animal Disease of Sichuan Province, College of Veterinary Medicine, Sichuang Agricultural University, Chengdu Sichuang, China
- * E-mail:
| | - Hengmin Cui
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, Key Laboratory of Environmental Hazard and Animal Disease of Sichuan Province, College of Veterinary Medicine, Sichuang Agricultural University, Chengdu Sichuang, China
| | - Yanchun Hu
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, Key Laboratory of Environmental Hazard and Animal Disease of Sichuan Province, College of Veterinary Medicine, Sichuang Agricultural University, Chengdu Sichuang, China
| | - Xiaoping Ma
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, Key Laboratory of Environmental Hazard and Animal Disease of Sichuan Province, College of Veterinary Medicine, Sichuang Agricultural University, Chengdu Sichuang, China
| | - Jing Fang
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, Key Laboratory of Environmental Hazard and Animal Disease of Sichuan Province, College of Veterinary Medicine, Sichuang Agricultural University, Chengdu Sichuang, China
| |
Collapse
|
23
|
Xin J, Chai Z, Zhang C, Zhang Q, Zhu Y, Cao H, Zhong J, Ji Q. Comparing the Microbial Community in Four Stomach of Dairy Cattle, Yellow Cattle and Three Yak Herds in Qinghai-Tibetan Plateau. Front Microbiol 2019; 10:1547. [PMID: 31354656 PMCID: PMC6636666 DOI: 10.3389/fmicb.2019.01547] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 06/20/2019] [Indexed: 01/06/2023] Open
Abstract
Yak (Bos grunniens) is an unique ruminant species in the Qinghai-Tibetan Plateau (QTP). The ruminant gastrointestinal tract (GIT) microbiota is not only associated with the nutrients metabolism, but also contributes to the host’s local adaptation. Examining the microbiota between cattle and yak in different geography could improve our understanding about the role of microbiota in metabolism and adaptation. To this end, we compared the microbiota in rumen, reticulum, omasum, and abomasum of dairy cattle, yellow cattle, and three yak herds (WQ yak, SZ yak, and ZB yak) lived in different altitude, based on sequencing the bacterial 16S rRNA gene on Illumina Miseq. The bacterial diversity was significantly different among five breeds, whereas the difference among four stomach regions is limited. The phyla Bacteroidetes and Firmicutes were the dominated bacteria regardless of breeds and regions. The nonmetric multidimensional scaling (NMDS) results showed that the microbiota in dairy cattle, yellow cattle and WQ yak significantly differed from that in SZ yak and ZB yak for all four stomach compartments. Canonical correlation analysis revealed that Prevotella and Succiniclasticum spp. were abundant in dairy cattle, yellow cattle and WQ yak, whereas the Christensenellaceae R7 group and the Lachnospiraceae UCG 008 group were prevalent in SZ yak and ZB yak. Moreover, the microbiota in WQ yak was significantly different from that in SZ yak and ZB yak, which were characterized by the higher relative abundance Romboutsia spp., Eubacterium coprostanoligenes, Acetobacter spp., Mycoplasma spp., and Rikenellaceae RC9 group. Overall, these results improves our knowledge about the GIT microbiota composition of QTP ruminant.
Collapse
Affiliation(s)
- Jinwei Xin
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Zhixin Chai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Chengfu Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Qiang Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Yong Zhu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Hanwen Cao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Qiumei Ji
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| |
Collapse
|
24
|
Ji YJ, Li H, Xie PF, Li ZH, Li HW, Yin YL, Blachier F, Kong XF. Stages of pregnancy and weaning influence the gut microbiota diversity and function in sows. J Appl Microbiol 2019; 127:867-879. [PMID: 31237071 PMCID: PMC6852164 DOI: 10.1111/jam.14344] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/07/2019] [Accepted: 05/14/2019] [Indexed: 12/17/2022]
Abstract
Aims The gut microbiota is believed to play important roles in the health of pregnant mammals, including their nutrient metabolism, immune programming and metabolic regulation. However, until recently, the shifts in gut microbiota composition and faecal and blood metabolic activity during different stages of pregnancy had not been investigated. Methods and Results We investigated the shifts in backfat thickness, plasma and faecal metabolites and gut microbiota on days 30, 60, 90 and 110 of pregnancy and on day 21 after parturition (weaning) in sows. The backfat thickness of sows did not significantly differ among the different stages of pregnancy. The plasma concentrations of lipid metabolites, including triacylglycerol (TG), total cholesterol, high‐density lipoprotein‐cholesterol, low‐density lipoprotein‐cholesterol and calcium were reduced (P < 0·05) during pregnancy. In addition, the concentration of these metabolites, except TG, reached their maximum at the time of weaning. We also found that Tenericutes, Fibrobacteres and Cyanobacteria varied significantly according to the stages of pregnancy in sows (P < 0·05). Most of the genera, such as Clostridiales, Desulfovibrio, Mogibacteriaceae and Prevotella, increased (P < 0·05) with the progression of pregnancy and decreased (P < 0·05) at weaning. The alpha diversity values (i.e., Shannon diversity and observed species) of sow gut microbiota increased (P < 0·05) from pregnancy to weaning. Pregnancy stages also significantly influenced (P < 0·05) the community structure (beta diversity) of gut microbiota. The progression of pregnancy was associated with changes in lipid metabolism and several carbohydrate‐degradation bacteria (i.e., Prevotella, Succinivibrio, Bacteroides and Parabacteroides). Conclusions Although causal links between the measured parameters remain hypothetical, these findings suggest that the increased diversity and concentration of beneficial gut microbes are associated with the metabolism of pregnant sows. Significance and Impact of the Study Manipulation of the sow gut microbiota composition may potentially influence metabolism and health during pregnancy.
Collapse
Affiliation(s)
- Y J Ji
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - H Li
- Institute of Occupational Health and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, China
| | - P F Xie
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Z H Li
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - H W Li
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Y L Yin
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - F Blachier
- UMR PNCA, AgroParisTech, INRA, Université Paris-Saclay, Paris, France
| | - X F Kong
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| |
Collapse
|
25
|
Heterogeneous development of methanogens and the correlation with bacteria in the rumen and cecum of sika deer (Cervus nippon) during early life suggest different ecology relevance. BMC Microbiol 2019; 19:129. [PMID: 31185894 PMCID: PMC6560721 DOI: 10.1186/s12866-019-1504-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 05/31/2019] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Enteric methane from the ruminant livestock is a significant source in global greenhouse gas emissions, which is mainly generated by the methanogens inhabiting the rumen and cecum. Sika deer (Cervus nippon) not only produces less methane than bovine, but they also harbor a distinct methanogen community. Whereas, knowledge of methanogens colonization in the rumen and cecum of sika deer is relatively still unknown, which could provide more insights to the manipulation of gut microbiota during early life. RESULTS Here, we examined the development of bacteria and methanogens in the rumen and cecum of juvenile sika deer from birth to post-weaning (1 day, 42 days and 70 days, respectively) based on next generation sequencing. The results showed that the facultative anaerobic bacteria were decreased and the cellulolytic bacteria were increased. However, methanogens established soon after birth thrived through the whole developmental period, indicating a different succession process than bacteria in the GIT, and the limited role of age and dietary change on GIT methanogens. We also found Methanobrevibacter spp. (Mean relative abundance = 44.2%) and Methanocorpusculum spp. (Mean relative abundance = 57.5%) were dominated in the rumen and cecum, respectively. The methanogens also formed specific correlations with bacteria under different niches, suggesting a role of ecology niche on methanogen community. CONCLUSIONS This study contributes to our knowledge about the microbial succession in GIT of sika deer, that may facilitate the development of targeted strategies to improve GIT function of sika deer.
Collapse
|
26
|
Qian W, Ao W, Jia C, Li Z. Bacterial colonisation of reeds and cottonseed hulls in the rumen of Tarim red deer (Cervus elaphus yarkandensis). Antonie van Leeuwenhoek 2019; 112:1283-1296. [PMID: 30941531 DOI: 10.1007/s10482-019-01260-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 03/26/2019] [Indexed: 12/18/2022]
Abstract
The rumen microbiome contributes greatly to the degradation of plant fibres to volatile fatty acids and microbial products, affecting the health and productivity of ruminants. In this study, we investigated the dynamics of colonisation by bacterial communities attached to reeds and cottonseed hulls in the rumen of Tarim red deer, a native species distributed in the desert of the Tarim Basin. The reed and cottonseed hull samples incubated in nylon bags for 1, 6, 12, and 48 h were collected and used to examine the bacterial communities by next-generation sequencing of the bacterial 16S rRNA gene. Prevotella1 and Rikenellaceae RC9 were the most abundant taxa in both the reed and cottonseed hull groups at various times, indicating a key role of these organisms in rumen fermentation in Tarim red deer. The relative abundances of cellulolytic bacteria, such as members of Fibrobacter, Treponema 2, Ruminococcaceae NK4A214 and Succiniclasticum increased, while that of the genus Prevotella 1 decreased, with increasing incubation time in both reeds and cottonseed hulls. Moreover, the temporal changes in bacterial diversity between reeds and cottonseed hulls were different, as demonstrated by the variations in the taxa Ruminococcaceae UCG 010 and Papillibacter in the reed group and Sphaerochaeta and Erysipelotrichaceae UCG 004 in the cottonseed hull group; the abundances of these bacteria first decreased and then increased. In conclusion, our results reveal the dynamics of bacterial colonisation of reeds and cottonseed hulls in the rumen of Tarim red deer.
Collapse
Affiliation(s)
- Wenxi Qian
- College of Animal Science, Tarim University, Alar, 843300, China.,Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, Alar, 843300, China
| | - Weiping Ao
- College of Animal Science, Tarim University, Alar, 843300, China.,Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, Alar, 843300, China
| | - Cunhui Jia
- College of Animal Science, Tarim University, Alar, 843300, China.,Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, Alar, 843300, China
| | - Zhipeng Li
- Department of Special Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, 130112, Changchun, China.
| |
Collapse
|
27
|
Temporal fermentation and microbial community dynamics in rumens of sheep grazing a ryegrass-based pasture offered either in the morning or in the afternoon. Animal 2019; 13:2242-2251. [PMID: 30786945 DOI: 10.1017/s1751731119000168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Eight ruminally-fistulated wethers were used to examine the temporal effects of afternoon (PM; 1600h) v. morning (AM; 0800 h) allocation of fresh spring herbage from a perennial ryegrass (Lolium perenne L.)-based pasture on fermentation and microbial community dynamics. Herbage chemical composition was minimally affected by time of allocation, but daily mean ammonia concentrations were greater for the PM group. The 24-h pattern of ruminal fermentation (i.e. time of sampling relative to time of allocation), however, varied considerably for all fermentation variables (P⩽0.001). Most notably amongst ruminal fermentation characteristics, ammonia concentrations showed a substantial temporal variation; concentrations of ammonia were 1.7-, 2.0- and 2.2-fold greater in rumens of PM wethers at 4, 6 and 8h after allocation, respectively, compared with AM wethers. The relative abundances of archaeal and ciliate protozoal taxa were similar across allocation groups. In contrast, the relative abundances of members of the rumen bacterial community, like Prevotella 1 (P=0.04), Bacteroidales RF16 group (P=0.005) and Fibrobacter spp. (P=0.008) were greater for the AM group, whereas the relative abundance of Kandleria spp. was greater (P=0.04) for the PM group. Of these taxa, only Prevotella 1 (P=0.04) and Kandleria (P<0.001) showed a significant interaction between time of allocation and time of sampling relative to feed allocation. Relative abundances of Prevotella 1 were greater at 2h (P=0.05), 4h (P=0.003) and 6h (P=0.01) after AM allocation of new herbage, whereas relative abundances of Kandleria were greater at 2h (P=0.003) and 4h (P<0.001) after PM allocation. The early post-allocation rise in ammonia concentrations in PM rumens occurred simultaneously with sharp increases in the relative abundance of Kandleria spp. and with a decline in the relative abundance of Prevotella. All measures of fermentation and most microbial community composition data showed highly dynamic changes in concentrations and genus abundances, respectively, with substantial temporal changes occurring within the first 8h of allocating a new strip of herbage. The dynamic changes in the relative abundances of certain bacterial groups, in synchrony with a substantial diurnal variation in ammonia concentrations, has potential effects on the efficiency by which N is utilised by the grazing ruminant.
Collapse
|
28
|
Agematu H, Takahashi T, Hamano Y. Continuous volatile fatty acid production from lignocellulosic biomass by a novel rumen-mimetic bioprocess. J Biosci Bioeng 2017; 124:528-533. [DOI: 10.1016/j.jbiosc.2017.06.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 06/12/2017] [Accepted: 06/16/2017] [Indexed: 11/26/2022]
|
29
|
Use of antimicrobial peptides as a feed additive for juvenile goats. Sci Rep 2017; 7:12254. [PMID: 28947748 PMCID: PMC5612951 DOI: 10.1038/s41598-017-12394-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/08/2017] [Indexed: 12/21/2022] Open
Abstract
Although antimicrobial peptides (AMPs) have been used as feed additives, only a few studies have examined their use in ruminants. In this study, we evaluated the use of AMPs(recombinant swine defensin and a fly antibacterial peptide were mixed by 1:1) as a medicated feed additive for juvenile goats. Dietary treatments included control groups (group I: 300 g concentrate; group III: 600 g concentrate), and AMP-supplemented groups (group II: 300 g concentrate + 3.0 g AMPs; group IV: 600 g concentrate + 3.0 g AMPs). AMP-treated groups exhibited an increase in bacterial genera, including Fibrobacter, Anaerovibrio, and Succiniclasticum, and the ciliate genus Ophryoscolex; as well a reduction in bacterial genera, such as Selenomonas, Succinivibrio, and Treponema, and the ciliate genera Polyplastron, Entodinium, and Isotricha. The changes in Fibrobacter, Anaerovibrio, Ophryoscolex, Polyplastron, Entodinium, and Isotricha were related to the concentrate. AMP treatment led to increased body weight, average daily weight gain, enzymatic activity (pectinase, xylanase, and lipase), especially in the normal concentrate group, and influence on ruminal fermentation function. In addition, goats treated with AMPs had higher rumen microorganism diversity indices than the control groups. Our results demonstrate that AMPs can be utilized as feed additives for juvenile goats.
Collapse
|
30
|
Baba Y, Matsuki Y, Mori Y, Suyama Y, Tada C, Fukuda Y, Saito M, Nakai Y. Pretreatment of lignocellulosic biomass by cattle rumen fluid for methane production: Bacterial flora and enzyme activity analysis. J Biosci Bioeng 2017; 123:489-496. [DOI: 10.1016/j.jbiosc.2016.11.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/18/2016] [Accepted: 11/19/2016] [Indexed: 01/19/2023]
|
31
|
Burnet MC, Dohnalkova AC, Neumann AP, Lipton MS, Smith RD, Suen G, Callister SJ. Evaluating Models of Cellulose Degradation by Fibrobacter succinogenes S85. PLoS One 2015; 10:e0143809. [PMID: 26629814 PMCID: PMC4668043 DOI: 10.1371/journal.pone.0143809] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 11/10/2015] [Indexed: 11/18/2022] Open
Abstract
Fibrobacter succinogenes S85 is an anaerobic non-cellulosome utilizing cellulolytic bacterium originally isolated from the cow rumen microbial community. Efforts to elucidate its cellulolytic machinery have resulted in the proposal of numerous models which involve cell-surface attachment via a combination of cellulose-binding fibro-slime proteins and pili, the production of cellulolytic vesicles, and the entry of cellulose fibers into the periplasmic space. Here, we used a combination of RNA-sequencing, proteomics, and transmission electron microscopy (TEM) to further clarify the cellulolytic mechanism of F. succinogenes. Our RNA-sequence analysis shows that genes encoding type II and III secretion systems, fibro-slime proteins, and pili are differentially expressed on cellulose, relative to glucose. A subcellular fractionation of cells grown on cellulose revealed that carbohydrate active enzymes associated with cellulose deconstruction and fibro-slime proteins were greater in the extracellular medium, as compared to the periplasm and outer membrane fractions. TEMs of samples harvested at mid-exponential and stationary phases of growth on cellulose and glucose showed the presence of grooves in the cellulose between the bacterial cells and substrate, suggesting enzymes work extracellularly for cellulose degradation. Membrane vesicles were only observed in stationary phase cultures grown on cellulose. These results provide evidence that F. succinogenes attaches to cellulose fibers using fibro-slime and pili, produces cellulases, such as endoglucanases, that are secreted extracellularly using type II and III secretion systems, and degrades the cellulose into cellodextrins that are then imported back into the periplasm for further digestion by β-glucanases and other cellulases.
Collapse
Affiliation(s)
- Meagan C. Burnet
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America
| | - Alice C. Dohnalkova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America
| | - Anthony P. Neumann
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, 53706, United States of America
| | - Mary S. Lipton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, 53706, United States of America
- * E-mail: (SJC); (GS)
| | - Stephen J. Callister
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America
- * E-mail: (SJC); (GS)
| |
Collapse
|
32
|
Gharechahi J, Zahiri HS, Noghabi KA, Salekdeh GH. In-depth diversity analysis of the bacterial community resident in the camel rumen. Syst Appl Microbiol 2015; 38:67-76. [DOI: 10.1016/j.syapm.2014.09.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/25/2014] [Accepted: 09/26/2014] [Indexed: 10/24/2022]
|
33
|
Shepherd ML, Ponder MA, Burk AO, Milton SC, Swecker WS. Fibre digestibility, abundance of faecal bacteria and plasma acetate concentrations in overweight adult mares. J Nutr Sci 2014; 3:e10. [PMID: 25191602 PMCID: PMC4153333 DOI: 10.1017/jns.2014.8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 02/10/2014] [Accepted: 03/04/2014] [Indexed: 02/06/2023] Open
Abstract
The purpose of the present study was to compare digestibility of grass hay, faecal and plasma volatile fatty acid (VFA) concentrations, and faecal bacterial abundance in overweight and moderate-condition mares. Five overweight adult mixed-breed mares and five adult mixed-breed mares in moderate condition were housed individually and limit-fed orchard grass (Dactylis glomerata) hay at 20 g/kg body weight (as fed) daily for 14 d. Forage DM and fibre digestibility were determined using AOAC methods; digestible energy was measured using bomb calorimetry; plasma and faecal VFA concentrations were determined by use of GC and MS; faecal Firmicutes, Bacteroidetes, Fibrobacter succinogenes, Ruminococcus flavefaciens and total bacteria abundance was determined by quantitative real-time PCR using previously designed phylum-specific 16S ribosomal RNA gene primers. No differences in hay digestibility, faecal VFA concentrations or faecal bacterial abundance were detected between overweight and moderate-condition mares. Mean plasma acetate concentrations were higher (P = 0·03) in overweight (1·55 (range 1·43-1·65) mmol/l) v. moderate-condition (1·39 (range 1·22-1·47) mmol/l) mares. We conclude that the higher plasma acetate in overweight mares should be further investigated as a potential link between gut microbes and obesity in horses.
Collapse
Affiliation(s)
- Megan L. Shepherd
- Department of Large Animal Clinical
Sciences, Virginia-Maryland Regional College of Veterinary
Medicine, Virginia Tech, Duck Pond Drive (0442), Blacksburg, VA
24061, USA
| | - Monica A. Ponder
- Department of Food Science and
Technology, Virginia Tech, Blacksburg, VA
24061, USA
| | - Amy O. Burk
- Department of Animal and Avian Sciences,
University of Maryland, College Park, MD
20742, USA
| | - Stewart C. Milton
- Department of Large Animal Clinical
Sciences, Virginia-Maryland Regional College of Veterinary
Medicine, Virginia Tech, Duck Pond Drive (0442), Blacksburg, VA
24061, USA
| | - William S. Swecker
- Department of Large Animal Clinical
Sciences, Virginia-Maryland Regional College of Veterinary
Medicine, Virginia Tech, Duck Pond Drive (0442), Blacksburg, VA
24061, USA
| |
Collapse
|
34
|
A phylogenetic analysis of the phylum Fibrobacteres. Syst Appl Microbiol 2013; 36:376-82. [PMID: 23759599 DOI: 10.1016/j.syapm.2013.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 04/03/2013] [Accepted: 04/19/2013] [Indexed: 11/21/2022]
Abstract
Members of the phylum Fibrobacteres are highly efficient cellulolytic bacteria, best known for their role in rumen function and as potential sources of novel enzymes for bioenergy applications. Despite being key members of ruminants and other digestive microbial communities, our knowledge of this phylum remains incomplete, as much of our understanding is focused on two recognized species, Fibrobacter succinogenes and F. intestinalis. As a result, we lack insights regarding the environmental niche, host range, and phylogenetic organization of this phylum. Here, we analyzed over 1000 16S rRNA Fibrobacteres sequences available from public databases to establish a phylogenetic framework for this phylum. We identify both species- and genus-level clades that are suggestive of previously unknown taxonomic relationships between Fibrobacteres in addition to their putative lifestyles as host-associated or free-living. Our results shed light on this poorly understood phylum and will be useful for elucidating the function, distribution, and diversity of these bacteria in their niches.
Collapse
|
35
|
HANIM CHUSNUL, MIRA YUSIATI LIES, NUR CAHYANTO MUHAMMAD, WIBOWO ALI. Mutagenic Improvement of Xylanase Production from Xylanolytic Bacteria and its Phylogenetic Analysis. MICROBIOLOGY INDONESIA 2013. [DOI: 10.5454/mi.7.2.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
36
|
Microbial community structure and dynamics during anaerobic digestion of various agricultural waste materials. Appl Microbiol Biotechnol 2013; 97:5161-74. [DOI: 10.1007/s00253-013-4867-0] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 03/18/2013] [Accepted: 03/20/2013] [Indexed: 10/26/2022]
|
37
|
Microbial ecosystem and fermentation traits in the caecum of growing rabbits given diets varying in neutral detergent soluble and insoluble fibre levels. Anaerobe 2013; 20:50-7. [PMID: 23403279 DOI: 10.1016/j.anaerobe.2013.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 01/21/2013] [Accepted: 02/01/2013] [Indexed: 11/23/2022]
Abstract
The effect of the level of neutral detergent fibre (NDF: 0.35, LI and 0.42, HI) and neutral detergent soluble fibre (NDSF: 0.14, LS and 0.17, HS) in the caecal ecosystem was studied in 24 weaned (28 days of age) rabbits, weighing 630 ± 80.2 g in a 2 × 2 factorial design. After 22 days, rabbits were slaughtered and their caecal contents sampled. The caecal pH (on average 6.2) and molar volatile fatty acids (VFA) proportions were not affected by dietary treatments, but total VFA concentration tended to be lower with NDF (84.7 vs. 74.1 mmol/l; P = 0.095). The amount of total bacteria tended (P = 0.075) to increase with NDSF, but only in diets with 0.35 NDF. The caecal proportions of Ruminococcus albus and Fibrobacter succinogenes were not affected by type or level of fibre, but Butyrivibrio fibrisolvens decreased (P = 0.055) with the NDF proportion in LS diets. Denaturing gradient gel electrophoresis (DGGE) analysis showed that bacterial communities clustered according to each combination of NDF and NDSF, but did not greatly differ among diets (similarity indexes between 0.67 and 0.70), nor biodiversity was affected (average Shannon and richness indexes 3.50 and 33.1; P > 0.10). Archaeal population revealed changes in the amount and composition that were particularly evident in HS diets, decreasing in concentration (from 4.37 to 4.12 log10 gene copy number/g) and biodiversity (Shannon index from 3.14 to 2.52 and richness index from 23.7 to 13.9) compared to LS. The type and level of dietary fibre had a minor impact on caecal fermentation traits or caecal bacterial community. However, the increase in NDSF from 0.14 to 0.17 reduced concentration and diversity of methanogenic archaea.
Collapse
|
38
|
Abstract
The role of microbes in fiber degradation and the relations among the microbes in sheep rumen were explored by in vivo elimination of fungi. The experiment was conducted on 6 Mongolian sheep with fistulae approximately 1.5 years old (35kg). The sheep were randomly divided into two groups, treatment group (n=3) and control group (n=3). The rumen fluids were collected from the rumen though fistulae. The results showed that the total numbers of bacteria, cellulolytic bacteria and protozoa in the rumen were significantly increased (P<0.05) after fungus elimination. Among the three main cellulolytic bacteria, the number of R.flavefaciens and F.succinogenes increased significant (P<0.05). Elimination of fungi significantly reduced the degradation of DM, NDF and ADF, and the activity of CMCase in sheep rumen (P<0.05). The number of total rumen bacteria and fungi detected by real-time PCR were about 10 times and 1,000 times higher than that of the traditional anaerobic culture method, suggesting that real-time PCR is superior to the traditional roller tube culture method.
Collapse
|
39
|
Fathallh Eida M, Nagaoka T, Wasaki J, Kouno K. Isolation and characterization of cellulose-decomposing bacteria inhabiting sawdust and coffee residue composts. Microbes Environ 2012; 27:226-33. [PMID: 22353767 PMCID: PMC4036048 DOI: 10.1264/jsme2.me11299] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Clarifying the identity and enzymatic activities of microorganisms associated with the decomposition of organic materials is expected to contribute to the evaluation and improvement of composting processes. In this study, we examined the cellulolytic and hemicellulolytic abilities of bacteria isolated from sawdust compost (SDC) and coffee residue compost (CRC). Cellulolytic bacteria were isolated using Dubos mineral salt agar containing azurine cross-linked (AZCL) HE-cellulose. Bacterial identification was performed based on the sequence analysis of 16S rRNA genes, and cellulase, xylanase, β-glucanase, mannanase, and protease activities were characterized using insoluble AZCL-linked substrates. Eleven isolates were obtained from SDC and 10 isolates from CRC. DNA analysis indicated that the isolates from SDC and CRC belonged to the genera Streptomyces, Microbispora, and Paenibacillus, and the genera Streptomyces, Microbispora, and Cohnella, respectively. Microbispora was the most dominant genus in both compost types. All isolates, with the exception of two isolates lacking mannanase activity, showed cellulase, xylanase, β-glucanase, and mannanase activities. Based on enzyme activities expressed as the ratio of hydrolysis zone diameter to colony diameter, it was suggested that the species of Microbispora (SDCB8, SDCB9) and Paenibacillus (SDCB10, SDCB11) in SDC and Microbispora (CRCB2, CRCB6) and Cohnella (CRCB9, CRCB10) in CRC contribute to efficient cellulolytic and hemicellulolytic processes during composting.
Collapse
|
40
|
Identification and Characterization of a Cellulase-Encoding Gene from the Buffalo Rumen Metagenomic Library. Biosci Biotechnol Biochem 2012; 76:1075-84. [DOI: 10.1271/bbb.110786] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
41
|
Wang P, Qi M, Barboza P, Leigh MB, Ungerfeld E, Selinger LB, McAllister TA, Forster RJ. Isolation of high-quality total RNA from rumen anaerobic bacteria and fungi, and subsequent detection of glycoside hydrolases. Can J Microbiol 2011; 57:590-8. [PMID: 21774582 DOI: 10.1139/w11-048] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The rumen is one of the most powerful fibrolytic fermentation systems known. Gene expression analyses, such as reverse transcription PCR (RT-PCR), microarrays, and metatranscriptomics, are techniques that could significantly expand our understanding of this ecosystem. The ability to isolate and stabilize representative RNA samples is critical to obtaining reliable results with these procedures. In this study, we successfully isolated high-quality total RNA from the solid phase of ruminal contents by using an improved RNA extraction method. This method is based on liquid nitrogen grinding of whole ruminal solids without microbial detachment and acid guanidinium - phenol - chloroform extraction combined with column purification. Yields of total RNA were as high as 150 µg per g of fresh ruminal content. The typical large subunit/small subunit rRNA ratio ranged from 1.8 to 2.0 with an RNA integrity number (Agilent Technologies) greater than 8.5. By eliminating the detachment step, the resulting RNA was more representative of the complete ecosystem. Our improved method removed a major barrier limiting analysis of rumen microbial function from a gene expression perspective. The polyA-tailed eukaryotic mRNAs obtained have successfully been applied to next-generation sequencing, and metatranscriptomic analysis of the solid fraction of rumen contents revealed abundant sequences related to rumen fungi.
Collapse
Affiliation(s)
- Pan Wang
- Agriculture and Agri-Food Canada, Lethbridge Research Centre
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Kim M, Morrison M, Yu Z. Status of the phylogenetic diversity census of ruminal microbiomes. FEMS Microbiol Ecol 2011; 76:49-63. [PMID: 21223325 DOI: 10.1111/j.1574-6941.2010.01029.x] [Citation(s) in RCA: 252] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In this study, the collective microbial diversity in the rumen was examined by performing a meta-analysis of all the curated 16S rRNA gene (rrn) sequences deposited in the RDP database. As of November 2010, 13,478 bacterial and 3516 archaeal rrn sequences were found. The bacterial sequences were assigned to 5271 operation taxonomic units (OTUs) at species level (0.03 phylogenetic distance) representing 19 existing phyla, of which the Firmicutes (2958 OTUs), Bacteroidetes (1610 OTUs) and Proteobacteria (226 OTUs) were the most predominant. These bacterial sequences were grouped into more than 3500 OTUs at genus level (0.05 distance), but only 180 existing genera were represented. Nearly all the archaeal sequences were assigned to 943 species-level OTUs in phylum Euryarchaeota. Although clustered into 670 genus-level OTUs, only 12 existing archaeal genera were represented. Based on rarefaction analysis, the current percent coverage at species level reached 71% for bacteria and 65% for archaea. At least 78,218 bacterial and 24,480 archaeal sequences would be needed to reach 99.9% coverage. The results of this study may serve as a framework to assess the significance of individual populations to rumen functions and to guide future studies to identify the alpha and global diversity of ruminal microbiomes.
Collapse
Affiliation(s)
- Minseok Kim
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA CSIRO Livestock Industries, St Lucia, Qld, Australia
| | | | | |
Collapse
|
43
|
Functional annotation of Fibrobacter succinogenes S85 carbohydrate active enzymes. Appl Biochem Biotechnol 2010; 163:649-57. [PMID: 20803100 DOI: 10.1007/s12010-010-9070-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2010] [Accepted: 08/16/2010] [Indexed: 10/19/2022]
Abstract
Fibrobacter succinogenes is a cellulolytic bacterium that degrades plant cell wall biomass in ruminant animals and is among the most rapidly fibrolytic of all mesophilic bacteria. The complete genome sequence of Fisuc was completed by the DOE Joint Genome Institute in late 2009. Using new expression tools developed at Lucigen and C5-6 Technologies and a multi-substrate screen, 5,760 random shotgun expression clones were screened for biomass-degrading enzymes, representing 2× genome expression coverage. From the screen, 169 positive hits were recorded and 33 were unambiguously identified by sequence analysis of the inserts as belonging to CAZy family genes. Eliminating duplicates, 24 unique CAZy genes were found by functional screening. Several previously uncharacterized enzymes were discovered using this approach and a number of potentially mis-annotated enzymes were functionally characterized. To complement this approach, a high-throughput system was developed to clone and express all the annotated glycosyl hydrolases and carbohydrate esterases in the genome. Using this method, six previously described and five novel CAZy enzymes were cloned, expressed, and purified in milligram quantities.
Collapse
|
44
|
Bacterial community diversity in paper mills processing recycled paper. J Ind Microbiol Biotechnol 2010; 37:1061-9. [DOI: 10.1007/s10295-010-0754-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Accepted: 05/20/2010] [Indexed: 10/19/2022]
|
45
|
Mirande C, Mosoni P, Béra-Maillet C, Bernalier-Donadille A, Forano E. Characterization of Xyn10A, a highly active xylanase from the human gut bacterium Bacteroides xylanisolvens XB1A. Appl Microbiol Biotechnol 2010; 87:2097-105. [PMID: 20532756 DOI: 10.1007/s00253-010-2694-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 05/18/2010] [Accepted: 05/19/2010] [Indexed: 01/08/2023]
Abstract
A xylanase gene xyn10A was isolated from the human gut bacterium Bacteroides xylanisolvens XB1A and the gene product was characterized. Xyn10A is a 40-kDa xylanase composed of a glycoside hydrolase family 10 catalytic domain with a signal peptide. A recombinant His-tagged Xyn10A was produced in Escherichia coli and purified. It was active on oat spelt and birchwood xylans and on wheat arabinoxylans. It cleaved xylotetraose, xylopentaose, and xylohexaose but not xylobiose, clearly indicating that Xyn10A is a xylanase. Surprisingly, it showed a low activity against carboxymethylcellulose but no activity at all against aryl-cellobioside and cellooligosaccharides. The enzyme exhibited K (m) and V (max) of 1.6 mg ml(-1) and 118 micromol min(-1) mg(-1) on oat spelt xylan, and its optimal temperature and pH for activity were 37 degrees C and pH 6.0, respectively. Its catalytic properties (k (cat)/K (m) = 3,300 ml mg(-1) min(-1)) suggested that Xyn10A is one of the most active GH10 xylanase described to date. Phylogenetic analyses showed that Xyn10A was closely related to other GH10 xylanases from human Bacteroides. The xyn10A gene was expressed in B. xylanisolvens XB1A cultured with glucose, xylose or xylans, and the protein was associated with the cells. Xyn10A is the first family 10 xylanase characterized from B. xylanisolvens XB1A.
Collapse
Affiliation(s)
- Caroline Mirande
- INRA, UR Unité de Microbiologie, Centre de Recherches de Clermont-Ferrand/Theix, Saint-Genès-Champanelle, France
| | | | | | | | | |
Collapse
|
46
|
Cellulosilyticum ruminicola, a newly described rumen bacterium that possesses redundant fibrolytic-protein-encoding genes and degrades lignocellulose with multiple carbohydrate- borne fibrolytic enzymes. Appl Environ Microbiol 2010; 76:3818-24. [PMID: 20400560 DOI: 10.1128/aem.03124-09] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cellulosilyticum ruminicola H1 is a newly described bacterium isolated from yak (Bos grunniens) rumen and is characterized by its ability to grow on a variety of hemicelluloses and degrade cellulosic materials. In this study, we performed the whole-genome sequencing of C. ruminicola H1 and observed a comprehensive set of genes encoding the enzymes essential for hydrolyzing plant cell wall. The corresponding enzymatic activities were also determined in strain H1; these included endoglucanases, cellobiohydrolases, xylanases, mannanase, pectinases, and feruloyl esterases and acetyl esterases to break the interbridge cross-link, as well as the enzymes that degrade the glycosidic bonds. This bacterium appears to produce polymer hydrolases that act on both soluble and crystal celluloses. Approximately half of the cellulytic activities, including cellobiohydrolase (50%), feruloyl esterase (45%), and one third of xylanase (31%) and endoglucanase (36%) activities were bound to cellulosic fibers. However, only a minority of mannase (6.78%) and pectinase (1.76%) activities were fiber associated. Strain H1 seems to degrade the plant-derived polysaccharides by producing individual fibrolytic enzymes, whereas the majority of polysaccharide hydrolases contain carbohydrate-binding module. Cellulosome or cellulosomelike protein complex was never isolated from this bacterium. Thus, the fibrolytic enzyme production of strain H1 may represent a different strategy in cellulase organization used by most of other ruminal microbes, but it applies the fungal mode of cellulose production.
Collapse
|
47
|
Mirande C, Kadlecikova E, Matulova M, Capek P, Bernalier-Donadille A, Forano E, Béra-Maillet C. Dietary fibre degradation and fermentation by two xylanolytic bacteria Bacteroides xylanisolvens XB1A and Roseburia intestinalis XB6B4 from the human intestine. J Appl Microbiol 2010; 109:451-460. [PMID: 20105245 DOI: 10.1111/j.1365-2672.2010.04671.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
AIMS To characterize fibre degradation, colonization and fermentation, and xylanase activity of two xylanolytic bacteria Bacteroides xylanisolvens XB1A(T) and Roseburia intestinalis XB6B4 from the human colon. METHODS AND RESULTS The bacteria grew well on all the substrates chosen to represent dietary fibres: wheat and corn bran, pea, cabbage and leek fibres, and also on purified xylans. Roseburia intestinalis colonized the substrates more efficiently than Bact. xylanisolvens. For the two bacteria, 80-99% of the total xylanase activity was associated with the cells whatever the substrate and time of growth. Optimal specific activities of cells were obtained on oat spelt xylan; they were higher than those previously measured for xylanolytic bacteria from the human gut. Roseburia intestinalis produced high molecular mass xylanases (100-70 kDa), while Bact. xylanisolvens produced lower molecular mass enzymes, including a cell-associated xylanase of 37 kDa. CONCLUSIONS The two bacteria display very high xylanolytic activity on the different substrates. Differences were observed on substrate attachment and enzyme systems, suggesting that the two species occupy different niches within the gut microbiota. SIGNIFICANCE AND IMPACT OF THE STUDY This study characterizes xylan degradation by two major species of the human intestine.
Collapse
Affiliation(s)
- C Mirande
- INRA, UR454 Unité de Microbiologie, Centre de Recherches de Clermont-Ferrand/Theix, Saint-Genès-Champanelle, France
| | - E Kadlecikova
- INRA, UR454 Unité de Microbiologie, Centre de Recherches de Clermont-Ferrand/Theix, Saint-Genès-Champanelle, France
| | - M Matulova
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - P Capek
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - A Bernalier-Donadille
- INRA, UR454 Unité de Microbiologie, Centre de Recherches de Clermont-Ferrand/Theix, Saint-Genès-Champanelle, France
| | - E Forano
- INRA, UR454 Unité de Microbiologie, Centre de Recherches de Clermont-Ferrand/Theix, Saint-Genès-Champanelle, France
| | - C Béra-Maillet
- INRA, UR454 Unité de Microbiologie, Centre de Recherches de Clermont-Ferrand/Theix, Saint-Genès-Champanelle, France
| |
Collapse
|
48
|
Béra-Maillet C, Mosoni P, Kwasiborski A, Suau F, Ribot Y, Forano E. Development of a RT-qPCR method for the quantification of Fibrobacter succinogenes S85 glycoside hydrolase transcripts in the rumen content of gnotobiotic and conventional sheep. J Microbiol Methods 2009; 77:8-16. [DOI: 10.1016/j.mimet.2008.11.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 11/22/2008] [Accepted: 11/23/2008] [Indexed: 10/21/2022]
|
49
|
Eneyskaya EV, Sundqvist G, Golubev AM, Ibatullin FM, Ivanen DR, Shabalin KA, Brumer H, Kulminskaya AA. Transglycosylating and hydrolytic activities of the beta-mannosidase from Trichoderma reesei. Biochimie 2009; 91:632-8. [PMID: 19327384 DOI: 10.1016/j.biochi.2009.03.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Accepted: 03/13/2009] [Indexed: 11/17/2022]
Abstract
A purified beta-mannosidase (EC 3.2.1.25) from the fungus Trichoderma reesei has been identified as a member of glycoside hydrolase family 2 through mass spectrometry analysis of tryptic peptides. In addition to hydrolysis, the enzyme catalyzes substrate transglycosylation with p-nitrophenyl beta-mannopyranoside. Structures of the major and minor products of this reaction were identified by NMR analysis as p-nitrophenyl mannobiosides and p-nitrophenyl mannotriosides containing beta-(1-->4) and beta-(1-->3) linkages. The rate of donor substrate hydrolysis increased in presence of acetonitrile and dimethylformamide, while transglycosylation was weakly suppressed by these organic solvents. Differential ultraviolet spectra of the protein indicate that a rearrangement of the hydrophobic environment of the active site following the addition of the organic solvents may be responsible for this hydrolytic activation.
Collapse
Affiliation(s)
- Elena V Eneyskaya
- Petersburg Nuclear Physics Institute, Russian Academy of Science, Molecular and Radiation Biophysics Division, Gatchina, Leningrad District, Russia
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Russell JB, Muck RE, Weimer PJ. Quantitative analysis of cellulose degradation and growth of cellulolytic bacteria in the rumen. FEMS Microbiol Ecol 2009; 67:183-97. [PMID: 19120465 DOI: 10.1111/j.1574-6941.2008.00633.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Ruminant animals digest cellulose via a symbiotic relationship with ruminal microorganisms. Because feedstuffs only remain in the rumen for a short time, the rate of cellulose digestion must be very rapid. This speed is facilitated by rumination, a process that returns food to the mouth to be rechewed. By decreasing particle size, the cellulose surface area can be increased by up to 10(6)-fold. The amount of cellulose digested is then a function of two competing rates, namely the digestion rate (K(d)) and the rate of passage of solids from the rumen (K(p)). Estimation of bacterial growth on cellulose is complicated by several factors: (1) energy must be expended for maintenance and growth of the cells, (2) only adherent cells are capable of degrading cellulose and (3) adherent cells can provide nonadherent cells with cellodextrins. Additionally, when ruminants are fed large amounts of cereal grain along with fiber, ruminal pH can decrease to a point where cellulolytic bacteria no longer grow. A dynamic model based on STELLA software is presented. This model evaluates all of the major aspects of ruminal cellulose degradation: (1) ingestion, digestion and passage of feed particles, (2) maintenance and growth of cellulolytic bacteria and (3) pH effects.
Collapse
Affiliation(s)
- James B Russell
- Plant, Soil and Nutrition Laboratory, Agricultural Research Service, USDA, Robert C. Holley Research Center, Ithaca, NY 14853, USA.
| | | | | |
Collapse
|