1
|
Rabapane KJ, Matambo TS. Profiling the dynamic adaptations of CAZyme-Producing microorganisms in the gastrointestinal tract of South African goats. Heliyon 2024; 10:e37508. [PMID: 39290285 PMCID: PMC11407064 DOI: 10.1016/j.heliyon.2024.e37508] [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: 10/09/2023] [Revised: 08/25/2024] [Accepted: 09/04/2024] [Indexed: 09/19/2024] Open
Abstract
The gastrointestinal tract of goats serves as a habitat for anaerobic microbial populations that work together to break down complex plant material, including lignocellulose. This study explored the microbial diversity and metabolic profiles across different gastrointestinal tract compartments. Significant diversity differences among the compartments were observed (ANOSIM p < 0.006), with the abomasum showing a distinct species composition and a decreased alpha diversity (Mann-Whitney/Kruskal-Wallis test p = 0.00096), possibly due to its acidic environment. Dominant microbial phyla included Proteobacteria, Bacteroidetes, and Firmicutes, with Proteobacteria being the most prevalent in the abomasum (50.06 %). Genera like Proteus and Bacteroides were particularly prominent in the rumen and reticulum, highlighting their significant role in feed degradation and fermentation processes. Over 65 % of genes at Kyoto Encyclopedia of Genes and Genomes level 1 were involved in metabolism with significant xenobiotic biodegradation in the abomasum. The dbCAN2 search identified Glycoside Hydrolases as the most prevalent CAZyme class (79 %), followed by Glycosyltransferases, Polysaccharide Lyases, and Carbohydrate Esterases, with Carbohydrate-Binding Modules and Auxiliary Activities accounting for 1 % of the hits. Higher CAZyme abundance was observed in the reticulum and omasum compartments, possibly due to MAGs diversity. In conclusion, the gastrointestinal tract of South African goats harbors diverse CAZyme classes, with Glycoside Hydrolases predominating. Interestingly, higher CAZyme abundance in specific compartments suggested compartmentalized microbial activity, reflecting adaptation to dietary substrates.
Collapse
Affiliation(s)
- Kgodiso J Rabapane
- Centre of Competence in Environmental Biotechnology, Department of Environmental Science, University of South Africa's College of Agriculture and Environmental Science, Cnr Pioneer and Christian De Wet Roads, Private Bag X6, Florida, 1710, South Africa
- Institute for Catalysis and Energy Solutions, University of South Africa's College of Science, Engineering, and Technology, Cnr Pioneer and Christian De Wet Roads, Private Bag X6, Florida, 1710, South Africa
| | - Tonderayi S Matambo
- Centre of Competence in Environmental Biotechnology, Department of Environmental Science, University of South Africa's College of Agriculture and Environmental Science, Cnr Pioneer and Christian De Wet Roads, Private Bag X6, Florida, 1710, South Africa
| |
Collapse
|
2
|
Lakes JE, Fu X, Harvey BT, Neupane KR, Aryal SP, Ferrell JL, Flythe MD, Richards CI. Impact of nicotine and cotinine on macrophage inflammatory plasticity via vesicular modifications in gastrointestinal bacteria. Anaerobe 2023; 83:102787. [PMID: 37827238 PMCID: PMC10841519 DOI: 10.1016/j.anaerobe.2023.102787] [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: 05/17/2023] [Revised: 09/26/2023] [Accepted: 10/03/2023] [Indexed: 10/14/2023]
Abstract
OBJECTIVES This study aimed to elucidate mechanistic explanation(s) for compositional changes to enteric microbiota by determining the impacts of continuous nicotine/cotinine exposure on representative gastrointestinal bacteria and how these alterations impact innate immune cell plasticity. METHODS In vitro cultures of the gastrointestinal bacteria (Bacteroides fragilis 25285, Prevotella bryantii B14, and Acetoanaerobium sticklandii SR) were continuously exposed to nicotine or cotinine. Supernatant samples were collected for fermentation acid analysis. Vesicles were collected and analyzed for physiological changes in number, size, and total protein cargo. Cultured macrophages were stimulated to a tolerogenic phenotype, exposed to control or altered (nicotine or cotinine - exposed) vesicles, and inflammatory plasticity assessed via inflammatory cytokine production. RESULTS Nicotine/cotinine exposure differentially affected metabolism of all bacteria tested in a Gram (nicotine) and concentration-dependent (cotinine) manner. Physiological studies demonstrated changes in vesiculation number and protein cargo following nicotine/cotinine exposures. Continuous exposure to 1 μM nicotine and 10 μM cotinine concentrations reduced total protein cargo of Gram (-) - 25285 and B14 vesicles, while cotinine generally increased total protein in Gram (+) - SR vesicles. We found that theses physiological changes to the vesicles of 25285 and SR formed under nicotine and cotinine, respectively, challenged the plasticity of tolerogenic macrophages. Tolerogenic macrophages exposed to vesicles from 1 μM nicotine, and 5 or 10 μΜ cotinine cultures produced significantly less IL-12p70, TNFα, or KC/GRO, regardless of macrophage exposure to nicotine/cotinine. CONCLUSIONS Nicotine/cotinine exposure differentially alters bacterial metabolism and vesicle physiology, ultimately impacting the inflammatory response of tolerogenic macrophages.
Collapse
Affiliation(s)
- Jourdan E Lakes
- Department of Chemistry, College of Arts & Sciences, University of Kentucky, Lexington, KY, USA.
| | - Xu Fu
- Department of Chemistry, College of Arts & Sciences, University of Kentucky, Lexington, KY, USA.
| | - Brock T Harvey
- Department of Chemistry, College of Arts & Sciences, University of Kentucky, Lexington, KY, USA.
| | - Khaga R Neupane
- Department of Chemistry, College of Arts & Sciences, University of Kentucky, Lexington, KY, USA.
| | - Surya P Aryal
- Department of Chemistry, College of Arts & Sciences, University of Kentucky, Lexington, KY, USA.
| | - Jessica L Ferrell
- USDA Agricultural Research Service Forage-Animal Production Research Unit, Lexington, KY, USA.
| | - Michael D Flythe
- USDA Agricultural Research Service Forage-Animal Production Research Unit, Lexington, KY, USA; Department of Animal and Food Sciences, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA.
| | - Christopher I Richards
- Department of Chemistry, College of Arts & Sciences, University of Kentucky, Lexington, KY, USA.
| |
Collapse
|
3
|
Osorio-Doblado AM, Feldmann KP, Lourenco JM, Stewart RL, Smith WB, Tedeschi LO, Fluharty FL, Callaway TR. Forages and pastures symposium: forage biodegradation: advances in ruminal microbial ecology. J Anim Sci 2023; 101:skad178. [PMID: 37257501 PMCID: PMC10313095 DOI: 10.1093/jas/skad178] [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: 02/22/2023] [Accepted: 05/26/2023] [Indexed: 06/02/2023] Open
Abstract
The rumen microbial ecosystem provides ruminants a selective advantage, the ability to utilize forages, allowing them to flourish worldwide in various environments. For many years, our understanding of the ruminal microbial ecosystem was limited to understanding the microbes (usually only laboratory-amenable bacteria) grown in pure culture, meaning that much of our understanding of ruminal function remained a "black box." However, the ruminal degradation of plant cell walls is performed by a consortium of bacteria, archaea, protozoa, and fungi that produces a wide variety of carbohydrate-active enzymes (CAZymes) that are responsible for the catabolism of cellulose, hemicellulose, and pectin. The past 15 years have seen the development and implementation of numerous next-generation sequencing (NGS) approaches (e.g., pyrosequencing, Illumina, and shotgun sequencing), which have contributed significantly to a greater level of insight regarding the microbial ecology of ruminants fed a variety of forages. There has also been an increase in the utilization of liquid chromatography and mass spectrometry that revolutionized transcriptomic approaches, and further improvements in the measurement of fermentation intermediates and end products have advanced with metabolomics. These advanced NGS techniques along with other analytic approaches, such as metaproteomics, have been utilized to elucidate the specific role of microbial CAZymes in forage degradation. Other methods have provided new insights into dynamic changes in the ruminal microbial population fed different diets and how these changes impact the assortment of products presented to the host animal. As more omics-based data has accumulated on forage-fed ruminants, the sequence of events that occur during fiber colonization by the microbial consortium has become more apparent, with fungal populations and fibrolytic bacterial populations working in conjunction, as well as expanding understanding of the individual microbial contributions to degradation of plant cell walls and polysaccharide components. In the future, the ability to predict microbial population and enzymatic activity and end products will be able to support the development of dynamic predictive models of rumen forage degradation and fermentation. Consequently, it is imperative to understand the rumen's microbial population better to improve fiber degradation in ruminants and, thus, stimulate more sustainable production systems.
Collapse
Affiliation(s)
- A M Osorio-Doblado
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - K P Feldmann
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - J M Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - R L Stewart
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - W B Smith
- Department Animal Science, Auburn University, Auburn, AL, USA
| | - L O Tedeschi
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - F L Fluharty
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - T R Callaway
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| |
Collapse
|
4
|
Kang M, Chhetri G, Kim I, So Y, Seo T. Comparative genomic analyses of four novel Ramlibacter species and the cellulose-degrading properties of Ramlibacter cellulosilyticus sp. nov. Sci Rep 2022; 12:21233. [PMID: 36482214 PMCID: PMC9731981 DOI: 10.1038/s41598-022-25718-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
In this study, four novel bacterial strains, USB13T, AW1T, GTP1T, and HM2T, were isolated from various environments in Busan and Jeju Island, Republic of Korea. The 16S rRNA sequencing results indicated that the four novel strains belong to the genus Ramlibacter. All four strains were tested for their potential cellulolytic properties, where strain USB13T was identified as the only novel bacterium and the first within its genus to show cellulolytic activity. When tested, the highest activities of endoglucanase, exoglucanase, β-glucosidase, and filter paper cellulase (FPCase) were 1.91 IU/mL, 1.77 IU/mL, 0.76 IU/mL, and 1.12 IU/mL, respectively at pH 6.0. Comparisons of draft whole genome sequences (WGS) were also made using average nucleotide identity, digital DNA-DNA hybridization values, and average amino acid identity values, while whole genome comparison was visualized using the BLAST Ring Image Generator. The G + C contents of the strains ranged from 67.9 to 69.9%, while genome sizes ranged from 4.31 to 6.15 Mbp. Based on polyphasic evidence, the novel strains represent four new species within the genus Ramlibacter, for which the names Ramlibacter cellulosilyticus sp. nov. (type strain, USB13T = KACC 21656T = NBRC 114839T) Ramlibacter aurantiacus sp. nov. (type strain, AW1T = KACC 21544T = NBRC 114862T), Ramlibacter albus sp. nov. (type strain, GTP1T = KACC 21702T = NBRC 114488T), and Ramlibacter pallidus sp. nov. (type strain, HM2T = KCTC 82557T = NBRC 114489T) are proposed.
Collapse
Affiliation(s)
- Minchung Kang
- grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University-Seoul, Goyang, 10326 Korea
| | - Geeta Chhetri
- grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University-Seoul, Goyang, 10326 Korea
| | - Inhyup Kim
- grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University-Seoul, Goyang, 10326 Korea
| | - Yoonseop So
- grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University-Seoul, Goyang, 10326 Korea
| | - Taegun Seo
- grid.255168.d0000 0001 0671 5021Department of Life Science, Dongguk University-Seoul, Goyang, 10326 Korea
| |
Collapse
|
5
|
Rabapane KJ, Ijoma GN, Matambo TS. Insufficiency in functional genomics studies, data, and applications: A case study of bio-prospecting research in ruminant microbiome. Front Genet 2022; 13:946449. [PMID: 36118848 PMCID: PMC9472250 DOI: 10.3389/fgene.2022.946449] [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: 05/17/2022] [Accepted: 07/21/2022] [Indexed: 12/02/2022] Open
Abstract
Over the last two decades, biotechnology has advanced at a rapid pace, propelled by the incorporation of bio-products into various aspects of pharmaceuticals, industry, and the environment. These developments have sparked interest in the bioprospecting of microorganisms and their products in a variety of niche environments. Furthermore, the use of omics technologies has greatly aided our analyses of environmental samples by elucidating the microbial ecological framework, biochemical pathways, and bio-products. However, the more often overemphasis on taxonomic identification in most research publications, as well as the data associated with such studies, is detrimental to immediate industrial and commercial applications. This review identifies several factors that contribute to the complexity of sequence data analysis as potential barriers to the pragmatic application of functional genomics, utilizing recent research on ruminants to demonstrate these limitations in the hopes of broadening our horizons and drawing attention to this gap in bioprospecting studies for other niche environments as well. The review also aims to emphasize the importance of routinely incorporating functional genomics into environmental metagenomics analyses in order to improve solutions that drive rapid industrial biocatalysis developments from derived outputs with the aim of achieving potential benefits in energy-use reduction and environmental considerations for current and future applications.
Collapse
|
6
|
Abstract
The utilization of dietary cellulose by resident bacteria in the large intestine of mammals, both herbivores and omnivores (including humans), has been a subject of interest since the nineteenth century. Cellulolytic bacteria are key participants in this breakdown process of cellulose, which is otherwise indigestible by the host. They critically contribute to host nutrition and health through the production of short-chain fatty acids, in addition to maintaining the balance of intestinal microbiota. Despite this key role, cellulolytic bacteria have not been well studied. In this review, we first retrace the history of the discovery of cellulolytic bacteria in the large intestine. We then focus on the current knowledge of cellulolytic bacteria isolated from the large intestine of various animal species and humans and discuss the methods used for isolating these bacteria. Moreover, we summarize the enzymes and the mechanisms involved in cellulose degradation. Finally, we present the contribution of these bacteria to the host.
Collapse
Affiliation(s)
- Alicia Froidurot
- Université Bourgogne Franche–Comté, Institut Agro Dijon, PAM UMR A 02.102, Dijon, France,CONTACT Alicia Froidurot Université Bourgogne Franche–Comté, Institut Agro Dijon, PAM UMR A 02.102Dijon, France
| | - Véronique Julliand
- Université Bourgogne Franche–Comté, Institut Agro Dijon, PAM UMR A 02.102, Dijon, France
| |
Collapse
|
7
|
Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, Wang W, Song H, Huang B, Zhu N, Bi Y, Ma X, Zhan F, Wang L, Hu T, Zhou H, Hu Z, Zhou W, Zhao L, Chen J, Meng Y, Wang J, Lin Y, Yuan J, Xie Z, Ma J, Liu WJ, Wang D, Xu W, Holmes EC, Gao GF, Wu G, Chen W, Shi W, Tan W. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet 2020; 395:565-574. [PMID: 32007145 PMCID: PMC7159086 DOI: 10.1016/s0140-6736(20)30251-8] [Citation(s) in RCA: 7347] [Impact Index Per Article: 1836.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 01/26/2020] [Accepted: 01/27/2020] [Indexed: 12/02/2022]
Abstract
BACKGROUND In late December, 2019, patients presenting with viral pneumonia due to an unidentified microbial agent were reported in Wuhan, China. A novel coronavirus was subsequently identified as the causative pathogen, provisionally named 2019 novel coronavirus (2019-nCoV). As of Jan 26, 2020, more than 2000 cases of 2019-nCoV infection have been confirmed, most of which involved people living in or visiting Wuhan, and human-to-human transmission has been confirmed. METHODS We did next-generation sequencing of samples from bronchoalveolar lavage fluid and cultured isolates from nine inpatients, eight of whom had visited the Huanan seafood market in Wuhan. Complete and partial 2019-nCoV genome sequences were obtained from these individuals. Viral contigs were connected using Sanger sequencing to obtain the full-length genomes, with the terminal regions determined by rapid amplification of cDNA ends. Phylogenetic analysis of these 2019-nCoV genomes and those of other coronaviruses was used to determine the evolutionary history of the virus and help infer its likely origin. Homology modelling was done to explore the likely receptor-binding properties of the virus. FINDINGS The ten genome sequences of 2019-nCoV obtained from the nine patients were extremely similar, exhibiting more than 99·98% sequence identity. Notably, 2019-nCoV was closely related (with 88% identity) to two bat-derived severe acute respiratory syndrome (SARS)-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, collected in 2018 in Zhoushan, eastern China, but were more distant from SARS-CoV (about 79%) and MERS-CoV (about 50%). Phylogenetic analysis revealed that 2019-nCoV fell within the subgenus Sarbecovirus of the genus Betacoronavirus, with a relatively long branch length to its closest relatives bat-SL-CoVZC45 and bat-SL-CoVZXC21, and was genetically distinct from SARS-CoV. Notably, homology modelling revealed that 2019-nCoV had a similar receptor-binding domain structure to that of SARS-CoV, despite amino acid variation at some key residues. INTERPRETATION 2019-nCoV is sufficiently divergent from SARS-CoV to be considered a new human-infecting betacoronavirus. Although our phylogenetic analysis suggests that bats might be the original host of this virus, an animal sold at the seafood market in Wuhan might represent an intermediate host facilitating the emergence of the virus in humans. Importantly, structural analysis suggests that 2019-nCoV might be able to bind to the angiotensin-converting enzyme 2 receptor in humans. The future evolution, adaptation, and spread of this virus warrant urgent investigation. FUNDING National Key Research and Development Program of China, National Major Project for Control and Prevention of Infectious Disease in China, Chinese Academy of Sciences, Shandong First Medical University.
Collapse
Affiliation(s)
- Roujian Lu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiang Zhao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Juan Li
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, China
| | - Peihua Niu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Bo Yang
- Division for Viral Disease Detection, Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Honglong Wu
- BGI PathoGenesis Pharmaceutical Technology, Shenzhen, China
| | - Wenling Wang
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hao Song
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Baoying Huang
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Na Zhu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuhai Bi
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing, China
| | - Xuejun Ma
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Faxian Zhan
- Division for Viral Disease Detection, Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Liang Wang
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing, China
| | - Tao Hu
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, China
| | - Hong Zhou
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, China
| | - Zhenhong Hu
- Central Theater, People's Liberation Army General Hospital, Wuhan, China
| | - Weimin Zhou
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Li Zhao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jing Chen
- Key Laboratory of Laboratory Medicine, Ministry of Education, and Zhejiang Provincial Key Laboratory of Medical Genetics, Institute of Medical Virology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yao Meng
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ji Wang
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yang Lin
- BGI PathoGenesis Pharmaceutical Technology, Shenzhen, China
| | - Jianying Yuan
- BGI PathoGenesis Pharmaceutical Technology, Shenzhen, China
| | - Zhihao Xie
- BGI PathoGenesis Pharmaceutical Technology, Shenzhen, China
| | - Jinmin Ma
- BGI PathoGenesis Pharmaceutical Technology, Shenzhen, China
| | - William J Liu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dayan Wang
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wenbo Xu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - George F Gao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing, China
| | - Guizhen Wu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Weijun Chen
- BGI PathoGenesis Pharmaceutical Technology, Shenzhen, China
| | - Weifeng Shi
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, China; The First Affiliated Hospital of Shandong First Medical University (Shandong Provincial Qianfoshan Hospital), Jinan, China.
| | - Wenjie Tan
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; Central Theater, People's Liberation Army General Hospital, Wuhan, China; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
8
|
Lakes JE, Richards CI, Flythe MD. Inhibition of Bacteroidetes and Firmicutes by select phytochemicals. Anaerobe 2019; 61:102145. [PMID: 31918362 DOI: 10.1016/j.anaerobe.2019.102145] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/11/2019] [Accepted: 12/23/2019] [Indexed: 01/26/2023]
Abstract
Current research indicates that changes in gut microbiota can impact the host, but it is not always clear how dietary and environmental factors alter gut microbiota. One potential factor is antimicrobial activity of compounds ingested by the host. The goal of this study was to determine the antimicrobial activity of common plant secondary metabolites against pure cultures of paired, structurally and phylogenetically distinct gastrointestinal bacteria of human or bovine origin: Prevotella bryantii B14, Bacteroides fragilis 25285, Acetoanaerobium (Clostridium) sticklandii SR and Clostridioides difficile 9689. When growth media were amended with individual phytochemicals (the alkaloids: berberine, capsaicin, nicotine, piperine and quinine and the phenolic: curcumin), growth of each species was inhibited to varying degrees at the three greatest concentrations tested (0.10-10.00 mg mL-1). The viable cell numbers of all the cultures were reduced, ≥4-logs, by berberine at concentrations ≥1.00 mg mL-1. Quinine performed similarly to berberine for B14, 25285, and SR at the same concentrations. The other phytochemicals were inhibitory, but not as much as quinine or berberine. Nicotine had activity against all four species (≥2-log reduction in viable cell number at 10.00 mg mL-1), but had stronger activity against the Gram-positive bacteria, SR and 9689, (≥4-log reductions at 10.00 mg mL-1). In conclusion, the phytochemicals had varying spectra of antimicrobial activity. These results are consistent with the hypothesis that ingested phytochemicals have the ability to differentially impact gut microbiota through antimicrobial activity.
Collapse
Affiliation(s)
- Jourdan E Lakes
- Department of Chemistry, College of Arts & Sciences, University of Kentucky, Lexington, KY, USA
| | - Christopher I Richards
- Department of Chemistry, College of Arts & Sciences, University of Kentucky, Lexington, KY, USA
| | - Michael D Flythe
- USDA Agricultural Research Service Forage-Animal Production Research Unit, Lexington, KY, USA; Department of Animal and Food Sciences, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA.
| |
Collapse
|
9
|
Williams BA, Mikkelsen D, Flanagan BM, Gidley MJ. "Dietary fibre": moving beyond the "soluble/insoluble" classification for monogastric nutrition, with an emphasis on humans and pigs. J Anim Sci Biotechnol 2019; 10:45. [PMID: 31149336 PMCID: PMC6537190 DOI: 10.1186/s40104-019-0350-9] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 03/29/2019] [Indexed: 12/22/2022] Open
Abstract
This review describes dietary fibres originating from a range of foods, particularly in relation to their plant cell walls. It explores the categorization of dietary fibres into “soluble” or “insoluble”. It also emphasizes dietary fibre fermentability, in terms of describing how the gastro-intestinal tract (GIT) microbiota respond to a selection of fibres from these categories. Food is categorized into cereals, legumes, fruits and vegetables. Mention is also made of example whole foods and why differences in physico-chemical characteristics between “purified” and “non-purified” food components are important in terms of health. Lastly, recommendations are made as to how dietary fibre could be classified differently, in relation to its functionality in terms of fermentability, rather than only its solubility.
Collapse
Affiliation(s)
- Barbara A Williams
- The University of Queensland, QAAFI Centre for Nutrition and Food Sciences, St. Lucia campus, Brisbane, Qld 4070 Australia
| | - Deirdre Mikkelsen
- The University of Queensland, QAAFI Centre for Nutrition and Food Sciences, St. Lucia campus, Brisbane, Qld 4070 Australia
| | - Bernadine M Flanagan
- The University of Queensland, QAAFI Centre for Nutrition and Food Sciences, St. Lucia campus, Brisbane, Qld 4070 Australia
| | - Michael J Gidley
- The University of Queensland, QAAFI Centre for Nutrition and Food Sciences, St. Lucia campus, Brisbane, Qld 4070 Australia
| |
Collapse
|
10
|
Neumann AP, Suen G. The Phylogenomic Diversity of Herbivore-Associated Fibrobacter spp. Is Correlated to Lignocellulose-Degrading Potential. mSphere 2018; 3:e00593-18. [PMID: 30541780 PMCID: PMC6291624 DOI: 10.1128/msphere.00593-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 11/29/2018] [Indexed: 12/30/2022] Open
Abstract
Members of the genus Fibrobacter are cellulose-degrading bacteria and common constituents of the gastrointestinal microbiota of herbivores. Although considerable phylogenetic diversity is observed among members of this group, few functional differences explaining the distinct ecological distributions of specific phylotypes have been described. In this study, we sequenced and performed a comparative analysis of whole genomes from 38 novel Fibrobacter strains against the type strains for the two formally described Fibrobacter species F. succinogenes strain S85 and F. intestinalis strain NR9. Significant differences in the number of genes encoding carbohydrate-active enzyme families involved in plant cell wall polysaccharide degradation were observed among Fibrobacter phylotypes. F. succinogenes genomes were consistently enriched in genes encoding carbohydrate-active enzymes compared to those of F. intestinalis strains. Moreover, genomes of F. succinogenes phylotypes that are dominant in the rumen had significantly more genes annotated to major families involved in hemicellulose degradation (e.g., CE6, GH10, and GH43) than did the genomes of F. succinogenes phylotypes typically observed in the lower gut of large hindgut-fermenting herbivores such as horses. Genes encoding a putative urease were also identified in 12 of the Fibrobacter genomes, which were primarily isolated from hindgut-fermenting hosts. Screening for growth on urea as the sole source of nitrogen provided strong evidence that the urease was active in these strains. These results represent the strongest evidence reported to date for specific functional differences contributing to the ecology of Fibrobacter spp. in the herbivore gut.IMPORTANCE The herbivore gut microbiome is incredibly diverse, and a functional understanding of this diversity is needed to more reliably manipulate this community for specific gain, such as increased production in ruminant livestock. Microbial degraders of plant cell wall polysaccharides in the herbivore gut, particularly Fibrobacter spp., are of fundamental importance to their hosts for digestion of a diet consisting primarily of recalcitrant plant fibers. Considerable phylogenetic diversity exists among members of the genus Fibrobacter, but much of this diversity remains cryptic. Here, we used comparative genomics, applied to a diverse collection of recently isolated Fibrobacter strains, to identify a robust association between carbohydrate-active enzyme gene content and the Fibrobacter phylogeny. Our results provide the strongest evidence reported to date for functional differences among Fibrobacter phylotypes associated with either the rumen or the hindgut and emphasize the general significance of carbohydrate-active enzymes in the evolution of fiber-degrading bacteria.
Collapse
Affiliation(s)
- Anthony P Neumann
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| |
Collapse
|
11
|
Söllinger A, Tveit AT, Poulsen M, Noel SJ, Bengtsson M, Bernhardt J, Frydendahl Hellwing AL, Lund P, Riedel K, Schleper C, Højberg O, Urich T. Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation. mSystems 2018; 3:e00038-18. [PMID: 30116788 PMCID: PMC6081794 DOI: 10.1128/msystems.00038-18] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/20/2018] [Indexed: 12/29/2022] Open
Abstract
Ruminant livestock is a major source of the potent greenhouse gas methane. The complex rumen microbiome, consisting of bacteria, archaea, and microbial eukaryotes, facilitates anaerobic plant biomass degradation in the cow rumen, leading to methane emissions. Using an integrated approach combining multidomain quantitative metatranscriptomics with gas and volatile fatty acid (VFA) profiling, we aimed at obtaining the most comprehensive picture of the active rumen microbiome during feed degradation to date. Bacterial, archaeal, and eukaryotic biomass, but also methane emissions and VFA concentrations, increased drastically within an hour after feed intake. mRNA profiling revealed a dynamic response of carbohydrate-active enzyme transcripts, transcripts involved in VFA production and methanogenesis. While the relative abundances of functional transcripts did not mirror observed processes, such as methane emissions, transformation to mRNA abundance per gram of rumen fluid echoed ruminant processes. The microbiome composition was highly individual, with, e.g., ciliate, Neocallimastigaceae, Prevotellaceae, Succinivibrionaceae, and Fibrobacteraceae abundances differing between cows. Microbiome individuality was accompanied by inter- and intradomain multifunctional redundancy among microbiome members during feed degradation. This likely enabled the robust performance of the anaerobic degradation process in each rumen. Neocallimastigaceae and ciliates contributed an unexpectedly large share of transcripts for cellulose- and hemicellulose-degrading enzymes, respectively. Methyl-reducing but not CO2-reducing methanogens were positively correlated with methane emissions. While Methanomassiliicoccales switched from methanol to methylamines as electron acceptors, Methanosphaera became the dominating methanol-reducing methanogen. This study for the first time linked rumen meta-omics with processes and enabled holistic insights into the contribution of all microbiome members to feed degradation. IMPORTANCE Ruminant animals, such as cows, live in a tight symbiotic association with microorganisms, allowing them to feed on otherwise indigestible plant biomass as food sources. Methane is produced as an end product of the anaerobic feed degradation in ruminants and is emitted to the atmosphere, making ruminant animals among the major anthropogenic sources of the potent greenhouse gas methane. Using newly developed quantitative metatranscriptomics for holistic microbiome analysis, we here identified bacterial, archaeal, and eukaryotic key players and the short-term dynamics of the rumen microbiome during anaerobic plant biomass degradation and subsequent methane emissions. These novel insights might pave the way for novel ecologically and economically sustainable methane mitigation strategies, much needed in times of global climate change.
Collapse
Affiliation(s)
- Andrea Söllinger
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Alexander Tøsdal Tveit
- Department of Arctic and Marine Biology, the Arctic University of Norway, Tromsø, Norway
| | - Morten Poulsen
- Department of Animal Sciences, Aarhus University, Tjele, Denmark
| | | | - Mia Bengtsson
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Jörg Bernhardt
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | | | - Peter Lund
- Department of Animal Sciences, Aarhus University, Tjele, Denmark
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Christa Schleper
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Ole Højberg
- Department of Animal Sciences, Aarhus University, Tjele, Denmark
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| |
Collapse
|
12
|
Mitsumori M. Isolation of Cellulolytic Bacteria from the Rumen. Methods Mol Biol 2018; 1796:57-65. [PMID: 29856046 DOI: 10.1007/978-1-4939-7877-9_5] [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] [Indexed: 06/08/2023]
Abstract
To isolate strictly anaerobic rumen bacteria capable of degrading cellulose, environmental and nutritional conditions similar to the rumen environment should be simulated in vitro. One of the most useful techniques for isolating rumen bacteria is the roll-tube technique. In this chapter, the roll-tube technique for isolating cellulolytic rumen bacteria is briefly outlined.
Collapse
Affiliation(s)
- Makoto Mitsumori
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan.
| |
Collapse
|
13
|
Tapio I, Snelling TJ, Strozzi F, Wallace RJ. The ruminal microbiome associated with methane emissions from ruminant livestock. J Anim Sci Biotechnol 2017; 8:7. [PMID: 28123698 PMCID: PMC5244708 DOI: 10.1186/s40104-017-0141-0] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 01/03/2017] [Indexed: 02/06/2023] Open
Abstract
Methane emissions from ruminant livestock contribute significantly to the large environmental footprint of agriculture. The rumen is the principal source of methane, and certain features of the microbiome are associated with low/high methane phenotypes. Despite their primary role in methanogenesis, the abundance of archaea has only a weak correlation with methane emissions from individual animals. The composition of the archaeal community appears to have a stronger effect, with animals harbouring the Methanobrevibacter gottschalkii clade tending to be associated with greater methane emissions. Ciliate protozoa produce abundant H2, the main substrate for methanogenesis in the rumen, and their removal (defaunation) results in an average 11% lower methane emissions in vivo, but the results are not consistent. Different protozoal genera seem to result in greater methane emissions, though community types (A, AB, B and O) did not differ. Within the bacteria, three different ‘ruminotypes’ have been identified, two of which predispose animals to have lower methane emissions. The two low-methane ruminotypes are generally characterized by less abundant H2-producing bacteria. A lower abundance of Proteobacteria and differences in certain Bacteroidetes and anaerobic fungi seem to be associated with high methane emissions. Rumen anaerobic fungi produce abundant H2 and formate, and their abundance generally corresponds to the level of methane emissions. Thus, microbiome analysis is consistent with known pathways for H2 production and methanogenesis, but not yet in a predictive manner. The production and utilisation of formate by the ruminal microbiota is poorly understood and may be a source of variability between animals.
Collapse
Affiliation(s)
- Ilma Tapio
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
| | - Timothy J Snelling
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB16 5BD UK
| | | | - R John Wallace
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB16 5BD UK
| |
Collapse
|
14
|
Draft Genome Sequence of Clostridium sp. Strain W14A Isolated from a Cellulose-Degrading Biofilm in a Landfill Leachate Microcosm. GENOME ANNOUNCEMENTS 2016; 4:4/5/e00985-16. [PMID: 27660778 PMCID: PMC5034129 DOI: 10.1128/genomea.00985-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the draft genome of Clostridium sp. strain W14A, isolated from the anaerobic, cellulolytic biofilm of a cotton string sample incubated in a landfill leachate microcosm. The draft genome comprises 131 contigs, 3,823,510 bp, 51.5% G+C content, and 4,119 predicted coding domain sequences.
Collapse
|
15
|
Dehority BA. Microbial Ecology of Cell Wall Fermentation. FORAGE CELL WALL STRUCTURE AND DIGESTIBILITY 2015. [DOI: 10.2134/1993.foragecellwall.c17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
16
|
Ransom-Jones E, Jones DL, Edwards A, McDonald JE. Distribution and diversity of members of the bacterial phylum Fibrobacteres in environments where cellulose degradation occurs. Syst Appl Microbiol 2014; 37:502-9. [DOI: 10.1016/j.syapm.2014.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Revised: 06/10/2014] [Accepted: 06/10/2014] [Indexed: 10/25/2022]
|
17
|
Rajilić-Stojanović M, de Vos WM. The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiol Rev 2014; 38:996-1047. [PMID: 24861948 PMCID: PMC4262072 DOI: 10.1111/1574-6976.12075] [Citation(s) in RCA: 723] [Impact Index Per Article: 72.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/29/2014] [Accepted: 05/09/2014] [Indexed: 02/06/2023] Open
Abstract
The microorganisms that inhabit the human gastrointestinal tract comprise a complex ecosystem with functions that significantly contribute to our systemic metabolism and have an impact on health and disease. In line with its importance, the human gastrointestinal microbiota has been extensively studied. Despite the fact that a significant part of the intestinal microorganisms has not yet been cultured, presently over 1000 different microbial species that can reside in the human gastrointestinal tract have been identified. This review provides a systematic overview and detailed references of the total of 1057 intestinal species of Eukarya (92), Archaea (8) and Bacteria (957), based on the phylogenetic framework of their small subunit ribosomal RNA gene sequences. Moreover, it unifies knowledge about the prevalence, abundance, stability, physiology, genetics and the association with human health of these gastrointestinal microorganisms, which is currently scattered over a vast amount of literature published in the last 150 years. This detailed physiological and genetic information is expected to be instrumental in advancing our knowledge of the gastrointestinal microbiota. Moreover, it opens avenues for future comparative and functional metagenomic and other high-throughput approaches that need a systematic and physiological basis to have an impact.
Collapse
Affiliation(s)
- Mirjana Rajilić-Stojanović
- Department for Biotechnology and Biochemical Engineering, Faculty of Technology and Metallurgy, University of BelgradeBelgrade, Serbia
- Laboratory of Microbiology, Wageningen UniversityWageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen UniversityWageningen, The Netherlands
- Departments of Bacteriology and Immunology, and Veterinary Biosciences, University of HelsinkiHelsinki, Finland
| |
Collapse
|
18
|
Evaluation of native potential probiotic bacteria using an in vitro ruminal fermentation system. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0753-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
|
19
|
Nyonyo T, Shinkai T, Tajima A, Mitsumori M. Effect of media composition, including gelling agents, on isolation of previously uncultured rumen bacteria. Lett Appl Microbiol 2012; 56:63-70. [DOI: 10.1111/lam.12019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 10/18/2012] [Accepted: 10/18/2012] [Indexed: 11/29/2022]
Affiliation(s)
- T. Nyonyo
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba Ibaraki Japan
| | - T. Shinkai
- National Institute of Livestock and Grassland Science; Tsukuba Ibaraki Japan
| | - A. Tajima
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba Ibaraki Japan
| | - M. Mitsumori
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba Ibaraki Japan
- National Institute of Livestock and Grassland Science; Tsukuba Ibaraki Japan
| |
Collapse
|
20
|
Ransom-Jones E, Jones DL, McCarthy AJ, McDonald JE. The Fibrobacteres: an important phylum of cellulose-degrading bacteria. MICROBIAL ECOLOGY 2012; 63:267-81. [PMID: 22213055 DOI: 10.1007/s00248-011-9998-1] [Citation(s) in RCA: 193] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 12/12/2011] [Indexed: 05/05/2023]
Abstract
The phylum Fibrobacteres currently comprises one formal genus, Fibrobacter, and two cultured species, Fibrobacter succinogenes and Fibrobacter intestinalis, that are recognised as major bacterial degraders of lignocellulosic material in the herbivore gut. Historically, members of the genus Fibrobacter were thought to only occupy mammalian intestinal tracts. However, recent 16S rRNA gene-targeted molecular approaches have demonstrated that novel centres of variation within the genus Fibrobacter are present in landfill sites and freshwater lakes, and their relative abundance suggests a potential role for fibrobacters in cellulose degradation beyond the herbivore gut. Furthermore, a novel subphylum within the Fibrobacteres has been detected in the gut of wood-feeding termites, and proteomic analyses have confirmed their involvement in cellulose hydrolysis. The genome sequence of F. succinogenes rumen strain S85 has recently suggested that within this group of organisms a "third" way of attacking the most abundant form of organic carbon in the biosphere, cellulose, has evolved. This observation not only has evolutionary significance, but the superior efficiency of anaerobic cellulose hydrolysis by Fibrobacter spp., in comparison to other cellulolytic rumen bacteria that typically utilise membrane-bound enzyme complexes (cellulosomes), may be explained by this novel cellulase system. There are few bacterial phyla with potential functional importance for which there is such a paucity of phenotypic and functional data. In this review, we highlight current knowledge of the Fibrobacteres phylum, its taxonomy, phylogeny, ecology and potential as a source of novel glycosyl hydrolases of biotechnological importance.
Collapse
Affiliation(s)
- Emma Ransom-Jones
- School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | | | | | | |
Collapse
|
21
|
Abstract
The biodegradation of lignocellulose, the most abundant organic material in the biosphere, is a feature of many aerobic, facultatively anaerobic and obligately anaerobic bacteria and fungi. Despite widely recognized difficulties in the isolation and cultivation of individual microbial species from complex microbial populations and environments, significant progress has been made in recovering cellulolytic taxa from a range of ecological niches including the human, herbivore, and termite gut, and terrestrial, aquatic, and managed environments. Knowledge of cellulose-degrading microbial taxa is of significant importance with respect to nutrition, biodegradation, biotechnology, and the carbon-cycle, providing insights into the metabolism, physiology, and functional enzyme systems of the cellulolytic bacteria and fungi that are responsible for the largest flow of carbon in the biosphere. In this chapter, several strategies employed for the isolation and cultivation of cellulolytic microorganisms from oxic and anoxic environments are described.
Collapse
|
22
|
Boyle PM, Silver PA. Parts plus pipes: synthetic biology approaches to metabolic engineering. Metab Eng 2011; 14:223-32. [PMID: 22037345 DOI: 10.1016/j.ymben.2011.10.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 10/05/2011] [Accepted: 10/16/2011] [Indexed: 11/24/2022]
Abstract
Synthetic biologists combine modular biological "parts" to create higher-order devices. Metabolic engineers construct biological "pipes" by optimizing the microbial conversion of basic substrates to desired compounds. Many scientists work at the intersection of these two philosophies, employing synthetic devices to enhance metabolic engineering efforts. These integrated approaches promise to do more than simply improve product yields; they can expand the array of products that are tractable to produce biologically. In this review, we explore the application of synthetic biology techniques to next-generation metabolic engineering challenges, as well as the emerging engineering principles for biological design.
Collapse
Affiliation(s)
- Patrick M Boyle
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | | |
Collapse
|
23
|
Cunha IS, Barreto CC, Costa OYA, Bomfim MA, Castro AP, Kruger RH, Quirino BF. Bacteria and Archaea community structure in the rumen microbiome of goats (Capra hircus) from the semiarid region of Brazil. Anaerobe 2011; 17:118-24. [PMID: 21575735 DOI: 10.1016/j.anaerobe.2011.04.018] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 03/09/2011] [Accepted: 04/26/2011] [Indexed: 11/18/2022]
Abstract
Most studies present in the literature about the rumen microbiome have focused on cattle and sheep. This is the first report of the characterization of the bacterial and archaeal communities present in the liquid and solid-associated fractions of the rumen from free ranging Moxotó breed goats using 16S rRNA gene libraries. PCR was used to amplify the 16S rRNA gene with bacterial and archaeal universal primers and sequences from each library constructed were obtained. Sequences of Bacteria from the phyla Bacteroidetes and Firmicutes were predominant. The overall dominant classes in the rumen were Clostridia and Bacteroidia, which are known to play a role in plant fiber degradation in other ruminants. Unclassified Bacteria accounted for 4.7% of the liquid fraction sequences and 16.4% of the solid fraction sequences. From the archaeal libraries only sequences from the phylum Euryarcheota were identified and were assigned to the class Methanobacteria of the genera Methanobrevibacter and Methanosphaera. A group of Archaea not previously known to be associated with the rumen was identified: uncultured methanogens belonging to the "uncultured marine bacteria" groups II and III. The local water contained high salt concentrations and this may explain the presence of these groups in the Moxotó goat rumen.
Collapse
Affiliation(s)
- Isabel S Cunha
- Universidade Católica de Brasília, Genomic Sciences and Biotechnology Program, Brasília
| | | | | | | | | | | | | |
Collapse
|
24
|
Feng Y, Yu Y, Wang X, Qu Y, Li D, He W, Kim BH. Degradation of raw corn stover powder (RCSP) by an enriched microbial consortium and its community structure. BIORESOURCE TECHNOLOGY 2011; 102:742-7. [PMID: 20863696 DOI: 10.1016/j.biortech.2010.08.074] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Revised: 08/17/2010] [Accepted: 08/20/2010] [Indexed: 05/15/2023]
Abstract
A microbial consortium with a high cellulolytic activity was enriched to degrade raw corn stover powder (RCSP). This consortium degraded more than 51% of non-sterilized RCSP or 81% of non-sterilized filter paper within 8 days at 40°C under facultative anoxic conditions. Cellulosome-like structures were observed in scanning electron micrographs (SEM) of RCSP degradation residue. The high cellulolytic activity was maintained during 40 subcultures in a medium containing cellulosic substrate. Small ribosomal gene sequence analyses showed the consortium contains uncultured and cultured bacteria with or without cellulolytic activities. Among these bacteria, some are anaerobic others aerobic. Analyses of the culture filtrate showed a typical anoxic polysaccharide fermentation during the culturing process. Reducing sugar concentration increased at early stage followed by various fermentation products that were consumed at the late stage.
Collapse
Affiliation(s)
- Yujie Feng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No. 73 Huanghe Road, Nangang District, Harbin 150090, China.
| | | | | | | | | | | | | |
Collapse
|
25
|
Forsberg CW, Beveridge TJ, Hellstrom A. Cellulase and Xylanase Release from Bacteroides succinogenes and Its Importance in the Rumen Environment. Appl Environ Microbiol 2010; 42:886-96. [PMID: 16345891 PMCID: PMC244123 DOI: 10.1128/aem.42.5.886-896.1981] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During growth of Bacteroides succinogenes in a liquid medium with cellulose as the source of carbohydrate, greater than 80% of the carboxymethylcellulase (endo-beta-1,4-glucanase), xylanase, and aryl-beta-xylosidase and 50% of the aryl-beta-glucosidase released from cells into the culture fluid. Less than 25% of the cellobiase activity was detected in the culture fluid. Approximately 50% of each of the released enzymes measured was associated with sedimentable subcellular membrane vesicles. The vesicles appeared to be released from the outer membrane of intact cells by bleb formation, primarily in pockets between the cells and the cellulose, although a few unattached cells with blebs were seen. Many vesicles were seen adhering to cellulose, and they were also seen free in the culture fluid. These data suggest that B. succinogenes releases hydrolytic enzymes in nonsedimentable and particulate forms during growth by a mechanism which has until now received little attention. Cellulose incubated in a porous nylon bag in the rumen was colonized by bacteria resembling B. succinogenes, and subcellular vesicles were seen penetrating channels and fractures in the cellulose. On this basis, it is suggested that B. succinogenes cells in the rumen contribute to an extracellular population of subcellular vesicles that possess cellulolytic and hemicellulolytic activities which probably enhance polymer digestion and provide a source of sugars for microbes lacking polymer-degrading activity, thereby contributing to a stable heterogeneous microbial population.
Collapse
Affiliation(s)
- C W Forsberg
- Department of Microbiology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | | | | |
Collapse
|
26
|
Dinsdale D, Morris EJ, Bacon JS. Electron microscopy of the microbial populations present and their modes of attack on various cellulosic substrates undergoing digestion in the sheep rumen. Appl Environ Microbiol 2010; 36:160-8. [PMID: 16345303 PMCID: PMC243047 DOI: 10.1128/aem.36.1.160-168.1978] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cotton fibers and various cell wall preparations from grass leaves and from the feces of sheep fed on dried grass were placed in the sheep rumen in bags made from 5-mum-mesh nylon cloth. After periods of from 3 to 48 h, bags were removed, and the contents were fixed, embedded, sectioned, and stained for electron microscopy. Some of the bacteria present were seen to be closely associated with the cell walls, either tunneling within them or making very close contact. Evidence was obtained for differential digestion of cell walls and of the layers within them. Distinct differences were noticed between bacterial populations attacking the more susceptible wall types and those attacking feces cell walls and cotton fibers. Among the latter, the dominant form was a long, thin rod with a typical gramnegative cell wall structure, different from that described for Bacteroides succinogenes S85 or for Butyrivibrio fibrisolvens.
Collapse
Affiliation(s)
- D Dinsdale
- The Rowett Research Institute, Bucksburn, Aberdeen AB2 9SB, United Kingdom
| | | | | |
Collapse
|
27
|
Flythe M, Kagan I. Antimicrobial effect of red clover (Trifolium pratense) phenolic extract on the ruminal hyper ammonia-producing bacterium, Clostridium sticklandii. Curr Microbiol 2010; 61:125-31. [PMID: 20087740 DOI: 10.1007/s00284-010-9586-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Accepted: 01/08/2010] [Indexed: 11/28/2022]
Abstract
Ruminal proteolysis and subsequent amino acid degradation represent considerable economic loss in ruminant production. The hyper ammonia-producing bacteria (HAB) are largely responsible for amino acid deamination in the rumen. HAB can be controlled with ionophores, but they are also susceptible to antimicrobial plant secondary metabolites. Red clover (Trifolium pratense) is rich in soluble phenolics, and it is also more resistant to proteolysis than other legumes. The goal of this study was to identify phenolic compounds from Trifolium pratense cultivar Kenland, and determine if any of the compounds possessed antimicrobial activity against the bovine HAB, Clostridium sticklandii SR. HPLC analysis revealed that clover tissues were rich in the isoflavonoids formononetin and biochanin A, particularly in plants left to wilt for 24 h. Biochanin A inhibited C. sticklandii in bioassays that employed thin-layer chromatography (TLC). Both clover extracts and biochanin A inhibited the growth of C. sticklandii in broth culture, but formononetin had no effect. These results indicate that clover phenolic compounds may have a role in preventing amino acid fermentation.
Collapse
|
28
|
|
29
|
Berg Miller ME, Antonopoulos DA, Rincon MT, Band M, Bari A, Akraiko T, Hernandez A, Thimmapuram J, Henrissat B, Coutinho PM, Borovok I, Jindou S, Lamed R, Flint HJ, Bayer EA, White BA. Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1. PLoS One 2009; 4:e6650. [PMID: 19680555 PMCID: PMC2721979 DOI: 10.1371/journal.pone.0006650] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Accepted: 07/07/2009] [Indexed: 11/19/2022] Open
Abstract
Background Ruminococcus flavefaciens is a predominant cellulolytic rumen bacterium, which forms a multi-enzyme cellulosome complex that could play an integral role in the ability of this bacterium to degrade plant cell wall polysaccharides. Identifying the major enzyme types involved in plant cell wall degradation is essential for gaining a better understanding of the cellulolytic capabilities of this organism as well as highlighting potential enzymes for application in improvement of livestock nutrition and for conversion of cellulosic biomass to liquid fuels. Methodology/Principal Findings The R. flavefaciens FD-1 genome was sequenced to 29x-coverage, based on pulsed-field gel electrophoresis estimates (4.4 Mb), and assembled into 119 contigs providing 4,576,399 bp of unique sequence. As much as 87.1% of the genome encodes ORFs, tRNA, rRNAs, or repeats. The GC content was calculated at 45%. A total of 4,339 ORFs was detected with an average gene length of 918 bp. The cellulosome model for R. flavefaciens was further refined by sequence analysis, with at least 225 dockerin-containing ORFs, including previously characterized cohesin-containing scaffoldin molecules. These dockerin-containing ORFs encode a variety of catalytic modules including glycoside hydrolases (GHs), polysaccharide lyases, and carbohydrate esterases. Additionally, 56 ORFs encode proteins that contain carbohydrate-binding modules (CBMs). Functional microarray analysis of the genome revealed that 56 of the cellulosome-associated ORFs were up-regulated, 14 were down-regulated, 135 were unaffected, when R. flavefaciens FD-1 was grown on cellulose versus cellobiose. Three multi-modular xylanases (ORF01222, ORF03896, and ORF01315) exhibited the highest levels of up-regulation. Conclusions/Significance The genomic evidence indicates that R. flavefaciens FD-1 has the largest known number of fiber-degrading enzymes likely to be arranged in a cellulosome architecture. Functional analysis of the genome has revealed that the growth substrate drives expression of enzymes predicted to be involved in carbohydrate metabolism as well as expression and assembly of key cellulosomal enzyme components.
Collapse
Affiliation(s)
- Margret E. Berg Miller
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Dionysios A. Antonopoulos
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Marco T. Rincon
- Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Mark Band
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Albert Bari
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Tatsiana Akraiko
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Alvaro Hernandez
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jyothi Thimmapuram
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités Aix-Marseille I & II, Marseille, France
| | - Pedro M. Coutinho
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités Aix-Marseille I & II, Marseille, France
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Sadanari Jindou
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Harry J. Flint
- Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Edward A. Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Bryan A. White
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
| |
Collapse
|
30
|
Forano E, Delort AM, Matulova M. Carbohydrate metabolism inFibrobacter succinogenes: What NMR tells us. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2009. [DOI: 10.1080/08910600802106517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
| | | | - Maria Matulova
- Slovak Academy of Sciences, Institute of Chemistry, Center for Glycomics, Bratislava, Slovak Republic
| |
Collapse
|
31
|
|
32
|
WILSON MARIONK, BRIGGS CAE. THE NORMAL FLORA OF THE BOVINE RUMEN II. QUANTITATIVE BACTERIOLOGICAL STUDIES. ACTA ACUST UNITED AC 2008. [DOI: 10.1111/j.1365-2672.1955.tb02086.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
33
|
|
34
|
Affiliation(s)
- R H McBee
- Division of Industrial Research and Department of Bacteriology and Public Health, The State College of Washington, Pullman, Washington
| |
Collapse
|
35
|
Kosaric N, Blaszczyk R. Microbial aggregates in anaerobic wastewater treatment. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2005; 42:27-62. [PMID: 2291438 DOI: 10.1007/bfb0000730] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The phenomenon aggregation of anaerobic bacteria gives an opportunity to speed up the digestion rate during methanogenesis. The aggregates are mainly composed of methanogenic bacteria which convert acetate and H2/CO2 into methane. Other bacteria are also included in the aggregates but their concentration is rather small. The aggregates may also be formed during acetogenesis or even hydrolysis but such aggregates are not stable and disrupt quickly when not fed. A two stage process seems to be suitable when high concentrated solid waste must be treated. Special conditions are necessary to promote aggregate formation from methanogenic bacteria but aggregates once formed are stable without feeding even for a few years. The structure, texture and activity of bacterial aggregates depend on several parameters: (1)--temperature and pH, (2)--wastewater composition and (3)--hydrodynamic conditions within the reactor. The common influence of all these parameters is still rather unknown but some recommendations may be given. Temperature and pH should be maintained in the range which is optimal for methanogenic bacteria e.g. a temperature between 32 and 50 degrees C and a value pH between 6.5 and 7.5. Wastewaters should contain soluble wastes and the specific loading rate should be around one kgCOD(kgVSS)-1 d-1. The concentration of the elements influences aggregate composition and probably structure and texture. At high calcium concentration a change in the colour of the granules has been observed. Research is necessary to investigate the influence of other elements and organic toxicants on maintenance of the aggregates. Hydrodynamic conditions seem to influence the stability of the granules over long time periods. At low liquid stream rates, aggregates may starve and lysis within the aggregates is possible which results in hollowing of aggregates and their floating. At high liquid stream rates the aggregates may be disrupted and washed out of the reactor as a flocculent sludge. Methanogenic bacterial aggregates have been successfully applied in many full scale installations, especially for sugar beet, potato, pulp and paper mill, and other soluble wastes. The UASB reactors used for these treatments are simple in construction and handling which result in rather low total costs. A further and wider application of UASB reactors and methanogenic aggregates for various industrial wastewaters is expected.
Collapse
Affiliation(s)
- N Kosaric
- University of Western Ontario, Department of Chemical and Biochemical Engineering, London, Canada
| | | |
Collapse
|
36
|
Mould F, Morgan R, Kliem K, Krystallidou E. A review and simplification of the in vitro incubation medium. Anim Feed Sci Technol 2005. [DOI: 10.1016/j.anifeedsci.2005.05.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
37
|
|
38
|
Rincón MT, McCrae SI, Kirby J, Scott KP, Flint HJ. EndB, a multidomain family 44 cellulase from Ruminococcus flavefaciens 17, binds to cellulose via a novel cellulose-binding module and to another R. flavefaciens protein via a dockerin domain. Appl Environ Microbiol 2001; 67:4426-31. [PMID: 11571138 PMCID: PMC93185 DOI: 10.1128/aem.67.10.4426-4431.2001] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mechanisms by which cellulolytic enzymes and enzyme complexes in Ruminococcus spp. bind to cellulose are not fully understood. The product of the newly isolated cellulase gene endB from Ruminococcus flavefaciens 17 was purified as a His-tagged product after expression in Escherichia coli and found to be able to bind directly to crystalline cellulose. The ability to bind cellulose is shown to be associated with a novel cellulose-binding module (CBM) located within a region of 200 amino acids that is unrelated to known protein sequences. EndB (808 amino acids) also contains a catalytic domain belonging to glycoside hydrolase family 44 and a C-terminal dockerin-like domain. Purified EndB is also shown to bind specifically via its dockerin domain to a polypeptide of ca. 130 kDa present among supernatant proteins from Avicel-grown R. flavefaciens that attach to cellulose. The protein to which EndB attaches is a strong candidate for the scaffolding component of a cellulosome-like multienzyme complex recently identified in this species (S.-Y. Ding et al., J. Bacteriol. 183:1945-1953, 2001). It is concluded that binding of EndB to cellulose may occur both through its own CBM and potentially also through its involvement in a cellulosome complex.
Collapse
Affiliation(s)
- M T Rincón
- Rowett Research Institute, Bucksburn, Aberdeen AB21 9SB, United Kingdom
| | | | | | | | | |
Collapse
|
39
|
|
40
|
BRYANT MP, SMALL N, BOUMA C, ROBINSON IM. Characteristics of ruminal anaerobic celluloytic cocci and Cillobacterium cellulosolvens n. sp. J Bacteriol 2000; 76:529-37. [PMID: 13598714 PMCID: PMC290234 DOI: 10.1128/jb.76.5.529-537.1958] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
41
|
Abstract
With the development of strictly anaerobic techniques and habitat-simulating media, a variety of bacteria were isolated from the rumen in the 1940s and 1950s. Based on standard morphological and physiological characteristics, the microbial ecosystem of the rumen contains a very complex population of bacteria. In recent years, ruminal bacteria have been re-evaluated with newer, more objective, and genetically valid methods of classification. Ribosomes are complicated structures, and their DNA-encoding sequences are relatively free from selective pressure. Because ribosomes have evolved slowly, they provide a long-term natural history of evolution. The invariable and hypervariable regions of rRNA genes can be used to group bacteria into kingdoms, genera, and species. The 16S rRNA sequences have provided a basis for renaming some ruminal species (Bacteroides amylophilus is now Ruminobacter amylophilus and Bacteroides succinogenes is now Fibrobacter succinogenes) and for classifying at least one recently isolated ruminal bacterium (e.g., Clostridium aminophilum). The DNA:DNA hybridization is a more sensitive method of assessing bacterial relatedness than is 16S rRNA. Bacterial strains within a species should have a high degree of DNA:DNA homology, but some species of ruminal bacteria (e.g., Prevotella ruminicola and Butyrivibrio fibrisolvens) had highly unrelated strains. Studies of 16S rRNA and DNA:DNA hybridization indicate that the diversity of ruminal bacteria has been greatly underestimated. Traditional studies of phylogeny of ruminal bacteria were stymied by the fastidious growth requirements of many ruminal bacteria, and enumeration was tedious and inaccurate. Modern methods of bacterial classification do not require in vitro culture and have the potential of detecting even a single cell.
Collapse
|
42
|
McGavin M, Lam J, Forsberg CW. Regulation and distribution of Fibrobacter succinogenes subsp. succinogenes S85 endoglucanases. Appl Environ Microbiol 1990; 56:1235-44. [PMID: 2339882 PMCID: PMC184389 DOI: 10.1128/aem.56.5.1235-1244.1990] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The distribution of endoglucanase activities in cultures of Fibrobacter succinogenes subsp. succinogenes S85 grown on different carbon sources was examined by a variety of biochemical and immunological techniques. Total culture endoglucanase activity was primarily cell associated and was expressed constitutively, although synthesis of endoglucanase 1 (EG1) was repressed by cellobiose. Western immunoblotting showed that EG1 and EG3 were released into the culture fluid during growth, while EG2 remained largely associated with the cell. Subcellular localization showed low endoglucanase activity in the periplasmic fraction and similar, high levels in the cytoplasmic and membrane fractions. Western immunoblotting showed that EG2 was absent from the periplasmic fraction. Data from immunoelectron microscopy with either polyclonal or monoclonal antibody to EG2 revealed a high density of gold labeling at sites where there was a disruption in the regular features of the cell surface, such as in blebbing or physical tearing of the membrane. When cells were grown on cellulose, there was a high density of labeling on the cellulose but not on the cells, indicating that EG2 has limited exposure at the cell surface. On the basis of these data, export of enzymes from their intracellular locations appears to occur via three different mechanisms: a specific secretory pathway independent of cellulose, a secretory mechanism which is mediated by contact with cellulose, and a generalized blebbing process that occurs irrespective of the carbon source.
Collapse
Affiliation(s)
- M McGavin
- Department of Microbiology, University of Guelph, Ontario, Canada
| | | | | |
Collapse
|
43
|
Wedekind KJ, Mansfield HR, Montgomery L. Enumeration and isolation of cellulolytic and hemicellulolytic bacteria from human feces. Appl Environ Microbiol 1988; 54:1530-5. [PMID: 3415224 PMCID: PMC202691 DOI: 10.1128/aem.54.6.1530-1535.1988] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The fibrolytic microbiota of the human large intestine was examined to determine the numbers and types of cellulolytic and hemicellulolytic bacteria present. Fecal samples from each of five individuals contained bacteria capable of degrading the hydrated cellulose in spinach and in wheat straw pretreated with alkaline hydrogen peroxide (AHP-WS), whereas degradation of the relatively crystalline cellulose in Whatman no. 1 filter paper (PMC) was detected for only one of the five samples. The mean concentration of cellulolytic bacteria, estimated with AHP-WS as a substrate, was 1.2 X 10(8)/ml of feces. Pure cultures of bacteria isolated on AHP-WS were able to degrade PMC, indicating that interactions with other microbes were primarily responsible for previous low success rates in detecting fecal cellulolytic bacteria with PMC as a substrate. The cellulolytic bacteria included Ruminococcus spp., Clostridium sp., and two unidentified strains. The mean concentration of hemicellulolytic bacteria, estimated with larchwood xylan as a substrate, was 1.8 X 10(10)/ml of feces. The hemicellulose-degrading bacteria included Butyrivibrio sp., Clostridium sp., Bacteroides sp., and two unidentified strains, as well as four of the five cellulolytic strains. This work demonstrates that many humans harbor intestinal cellulolytic bacteria and that a hydrated cellulose source such as AHP-WS is necessary for their consistent detection and isolation.
Collapse
Affiliation(s)
- K J Wedekind
- Department of Animal Sciences, University of Illinois, Urbana 61801
| | | | | |
Collapse
|
44
|
Comparison of treatments for the in vitro detachment of cellulolytic bacteria from ruminal digesta samples. Curr Microbiol 1987. [DOI: 10.1007/bf01577259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
45
|
|
46
|
|
47
|
Abstract
Cellulose-degrading bacteria previously isolated from the ceca of rats have been characterized and identified. The most commonly isolated type was rods identified as Bacteroides succinogenes. These bacteria fermented only cellulose (e.g., pebble-milled Whatman no. 1 filter paper), cellobiose, and in 43 of 47 strains, glucose, with succinic and acetic acids as the major products. The only organic growth factors found to be required by selected strains were p-aminobenzoic acid, cyanocobalamine, thiamine, and a straight-chain and a branched-chain volatile fatty acid. These vitamin requirements differ from those of rumen strains of B. succinogenes, indicating the rat strains may form a distinct subgroup within the species. The mole percent guanine plus cytosine was 45%, a value lower than those (48 to 51%) found for three rumen strains of B. succinogenes included in this study. Cellulolytic cocci were isolated less frequently than the rods and were identified as Rumminococcus flavefaciens. Most strains fermented only cellulose and cellobiose, and their major fermentation products were also succinic and acetic acids. Their required growth factors were not identified but were supplied by rumen fluid.
Collapse
|
48
|
|
49
|
Abstract
This review describes the progress which has been made during the last 10 to 15 years in the field of rumen microbiology. It is basically an account of new discoveries in the bacteriology, protozoology, biochemistry, and ecology of the rumen microbial population. As such it covers a wide range of subjects including the isolation and properties of methanogenic bacteria, the role of rumen phycomycete fungi, anaerobic energy conservation, and general metabolic aspects of rumen microorganisms. It also attempts, however, to describe and develop new concepts in rumen microbiology. These consist principally of interactions of the microbemicrobe, microbe-food and microbe-host types, and represent the main areas of recent advance in our understanding of the rumen ecosystem. The development of experimental techniques such as chemostat culture and scanning electron microscopy are shown to have been instrumental in progress in these areas. The paper is concluded with an assessment of our present knowledge of the rumen fermentation, based on the degree of success of experiments with gnotobiotic ruminants inoculated with defined flora and in mathematical modeling of the fermentation. The efficacy of chemical manipulation of the fermentation in ruminant is also discussed in this light.
Collapse
|
50
|
Relative numbers of selected bacterial forms in different regions of the cockroach hindgut. Arch Microbiol 1981. [DOI: 10.1007/bf00455348] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|