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Li Z, Liu B, Cui H, Ding J, Li H, Xie G, Ren N, Xing D. The complete genome sequence of Ethanoligenens harbinense reveals the metabolic pathway of acetate-ethanol fermentation: A novel understanding of the principles of anaerobic biotechnology. Environ Int 2019; 131:105053. [PMID: 31357089 DOI: 10.1016/j.envint.2019.105053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/20/2019] [Accepted: 07/22/2019] [Indexed: 05/05/2023]
Abstract
Ethanol-type fermentation is one of three main fermentation types in the acidogenesis of anaerobic treatment systems. Non-spore-forming Ethanoligenens is as a typical genus capable of ethanol-type fermentation in mixed culture (i.e. acetate-ethanol fermentation). This genus can produce ethanol, acetate, CO2, and H2 using carbohydrates, and has application potential in anaerobic bioprocesses. Here, the complete genome sequences and methylome of Ethanoligenens harbinense strains with different autoaggregative and coaggregative abilities were obtained using the PacBio single-molecule real-time sequencing platform. The genome size of E. harbinense strains was about 2.97-3.10 Mb with 55.5% G+C content. 3020-3153 genes were annotated, most of which were methylated at specific sites or motifs. The methylation types included 6mA, 4mC, and unknown types. Comparative genomic analysis demonstrated low levels of genetic similarity between E. harbinense and other well-known hydrogen-producing bacteria (i.e., Clostridium and Thermoanaerobacter) in phylogenesis. Hydrogen production of E. harbinense was catalyzed by genes that encode [FeFe]‑hydrogenases and that were synthesized by three maturases of [FeFe]-H2ase. The metabolic mechanism of H2-ethanol co-production fermentation, catalyzed by pyruvate ferredoxin oxidoreductase was proposed. This study provides genetic and evolutionary information of a model genus for the further investigation of the metabolic pathway and regulatory network of ethanol-type fermentation and anaerobic bioprocesses for waste or wastewater treatment.
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Affiliation(s)
- Zhen Li
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Bingfeng Liu
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Han Cui
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jie Ding
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Huahua Li
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Guojun Xie
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nanqi Ren
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Defeng Xing
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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Liu R, Chen Y, Tian Z, Mao Z, Cheng H, Zhou H, Wang W. Enhancing microbial community performance on acid resistance by modified adaptive laboratory evolution. Bioresour Technol 2019; 287:121416. [PMID: 31103940 DOI: 10.1016/j.biortech.2019.121416] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/30/2019] [Accepted: 05/02/2019] [Indexed: 05/09/2023]
Abstract
A new strategy of three-step adaptive laboratory evolution (ALE) was developed to enhance the bioleaching performance of moderately thermophilic consortia. Through consortium construction, directed evolution and chemostat selection, an improved consortium (ALEend) that composed of Leptospirillum ferriphilum (80.32%), Sulfobacillus thermosulfidooxidans (15.82%) and Ferroplasma thermophilum (3.86%) was obtained, showing ferrous iron oxidation rate of 500 mgL-1h-1 and biomass production of 2.0 × 108 cells/mL at pH 0.75. During batch culturing, the ALEend consortium exhibited stable ferrous iron oxidation in wider conditions. PCA indicated that the communities were similar under fluctuating culture conditions, which demonstrated the stable community structure and the reinforced synergistic interactions resulting in the enhanced community performance. Pyrite bioleaching conducted at pH 1.5 and 0.75 revealed that the ALEend consortium extracted 26% and 55% more total iron relative to the original consortium. These findings indicated that the modified ALE may be a promising strategy for microbial community modification to enhance bioleaching.
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Affiliation(s)
- Ronghui Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yanzhi Chen
- South China Institute of Environmental Sciences, Guangzhou, China
| | - Zhuang Tian
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Zhenghua Mao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.
| | - Wei Wang
- South China Institute of Environmental Sciences, Guangzhou, China
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Wang S, Martins R, Sullivan MC, Friedman ES, Misic AM, El-Fahmawi A, De Martinis ECP, O'Brien K, Chen Y, Bradley C, Zhang G, Berry ASF, Hunter CA, Baldassano RN, Rondeau MP, Beiting DP. Diet-induced remission in chronic enteropathy is associated with altered microbial community structure and synthesis of secondary bile acids. Microbiome 2019; 7:126. [PMID: 31472697 PMCID: PMC6717631 DOI: 10.1186/s40168-019-0740-4] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/19/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND The microbiome has been implicated in the initiation and persistence of inflammatory bowel disease. Despite the fact that diet is one of the most potent modulators of microbiome composition and function and that dietary intervention is the first-line therapy for treating pediatric Crohn's disease, the relationships between diet-induced remission, enteropathy, and microbiome are poorly understood. Here, we leverage a naturally-occurring canine model of chronic inflammatory enteropathy that exhibits robust remission following nutritional therapy, to perform a longitudinal study that integrates clinical monitoring, 16S rRNA gene amplicon sequencing, metagenomic sequencing, metabolomic profiling, and whole genome sequencing to investigate the relationship between therapeutic diet, microbiome, and disease. RESULTS We show that remission induced by a hydrolyzed protein diet is accompanied by alterations in microbial community structure marked by decreased abundance of pathobionts (e.g., Escherichia coli and Clostridium perfringens), reduced severity of dysbiosis, and increased levels of the secondary bile acids, lithocholic and deoxycholic acid. Physiologic levels of these bile acids inhibited the growth of E. coli and C. perfringens isolates, in vitro. Metagenomic analysis and whole genome sequencing identified the bile acid producer Clostridium hiranonis as elevated after dietary therapy and a likely source of secondary bile acids during remission. When C. hiranonis was administered to mice, levels of deoxycholic acid were preserved and pathology associated with DSS colitis was ameliorated. Finally, a closely related bile acid producer, Clostridium scindens, was associated with diet-induced remission in human pediatric Crohn's disease. CONCLUSIONS These data highlight that remission induced by a hydrolyzed protein diet is associated with improved microbiota structure, an expansion of bile acid-producing clostridia, and increased levels of secondary bile acids. Our observations from clinical studies of exclusive enteral nutrition in human Crohn's disease, along with our in vitro inhibition assays and in vivo studies in mice, suggest that this may be a conserved response to diet therapy with the potential to ameliorate disease. These findings provide insight into diet-induced remission of gastrointestinal disease and could help guide the rational design of more effective therapeutic diets.
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Affiliation(s)
- Shuai Wang
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Rene Martins
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Megan C Sullivan
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Elliot S Friedman
- Division of Gastroenterology, School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ana M Misic
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ayah El-Fahmawi
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Kevin O'Brien
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ying Chen
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Charles Bradley
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Grace Zhang
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alexander S F Berry
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pediatric Gastroenterology Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Christopher A Hunter
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Robert N Baldassano
- Department of Pediatric Gastroenterology Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Mark P Rondeau
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Daniel P Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Sangavai C, Chellapandi P. A metabolic study to decipher amino acid catabolism-directed biofuel synthesis in Acetoanaerobium sticklandii DSM 519. Amino Acids 2019; 51:1397-1407. [PMID: 31471743 DOI: 10.1007/s00726-019-02777-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 08/22/2019] [Indexed: 01/15/2023]
Abstract
Acetoanaerobium sticklandii DSM 519 is a hyper-ammonia-producing anaerobe. It has the ability to produce organic solvents and acids from protein catabolism through Stickland reactions and specialized pathways. Nevertheless, its protein catabolism-directed biofuel production has not yet been understood. The present study aimed to decipher such growth-associated metabolic potential of this organism at different growth phases using metabolic profiling. A seed culture of this organism was grown separately in metabolic assay media supplemented with gelatin and or a mixture of amino acids. The extracellular metabolites produced by this organism were qualitatively analyzed by gas chromatography-mass spectrometry platform. The residual amino acids after protein degradation and amino acids assimilation were identified and quantitatively measured by high-performance liquid chromatography (HPLC). Organic solvents and acids produced by this organism were detected and the quantity of them determined with HPLC. Metabolic profiling data confirmed the presence of amino acid catabolic products including tyramine, cadaverine, methylamine, and putrescine in fermented broth. It also found products including short-chain fatty acids and organic solvents of the Stickland reactions. It reported that amino acids were more appropriate for its growth yield compared to gelatin. Results of quantitative analysis of amino acids indicated that many amino acids either from gelatin or amino acid mixture were catabolised at a log-growth phase. Glycine and proline were poorly consumed in all growth phases. This study revealed that apart from Stickland reactions, a specialized system was established in A. sticklandii for protein catabolism-directed biofuel production. Acetone-butanol-ethanol (ABE), acetic acid, and butyric acid were the most important biofuel components produced by this organism. The production of these components was achieved much more on gelatin than amino acids. Thus, A. sticklandii is suggested herein as a potential organism to produce butyric acid along with ABE from protein-based wastes (gelatin) in bio-energy sectors.
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Affiliation(s)
- C Sangavai
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
| | - P Chellapandi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India.
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Li H, Mei X, Liu B, Li Z, Wang B, Ren N, Xing D. Insights on acetate-ethanol fermentation by hydrogen-producing Ethanoligenens under acetic acid accumulation based on quantitative proteomics. Environ Int 2019; 129:1-9. [PMID: 31085357 DOI: 10.1016/j.envint.2019.05.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/29/2019] [Accepted: 05/06/2019] [Indexed: 06/09/2023]
Abstract
Ethanoligenens, a novel ethanologenic hydrogen-producing genus, is a representative fermenter in its unique acetate-ethanol fermentation and physiology. Acetic acid accumulation is one of major factors that affect H2-ethanol co-production. However, sufficient information is unavailable on the tolerance mechanisms of hydrogen-producing bacterium in acetic acid stress. The fermentation process of Ethanoligenens harbinense YUAN-3 was significantly slowed down in the selection stress of exogenous acetic acid. The maximum gas production rate of strain YUAN-3 decreased from 192.15 mL·(L-culture)-1·h-1 to 75.2 mL·(L-culture)-1·h-1 with increasing exogenous acetic acid from 0 mM to 30 mM, the batch fermentation period was correspondingly expanded from 66 h to 136 h. Through iTRAQ-based quantitative proteomic approach, 78, 121 and 216 proteins were differentially expressed after strain YUAN-3 was cultured in the medium supplemented with exogenous acetic acid of 10 mM, 20 mM and 30 mM. The up-regulated proteins were mainly involved in β-alanine and pyrimidine metabolism, oxidative stress response, while the down-regulated proteins mainly participated in phosphotransferase system (PTS), fructose and mannose metabolism, phosphate uptake, ribosome, and flagellar assembly. These proteins help to maintain balance between fermentation process and alleviation of intracellular acidification in strain YUAN-3. The study indicated that response to acetic acid stress in strain YUAN-3 was a complex process, which involved multiple metabolic pathways. Reductive pyrimidine catabolic pathway played an important role in the acetic acid resistance of E. harbinense.
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Affiliation(s)
- Huahua Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xiaoxue Mei
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Bingfeng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Zhen Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Baichen Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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Abreu AA, Tavares F, Alves MM, Cavaleiro AJ, Pereira MA. Garden and food waste co-fermentation for biohydrogen and biomethane production in a two-step hyperthermophilic-mesophilic process. Bioresour Technol 2019; 278:180-186. [PMID: 30703635 DOI: 10.1016/j.biortech.2019.01.085] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/15/2019] [Accepted: 01/19/2019] [Indexed: 06/09/2023]
Abstract
Co-fermentation of garden waste (GW) and food waste (FW) was assessed in a two-stage process coupling hyperthermophilic dark-fermentation and mesophilic anaerobic digestion (AD). In the first stage, biohydrogen production from individual substrates was tested at different volatile solids (VS) concentrations, using a pure culture of Caldicellulosiruptor saccharolyticus as inoculum. FW concentrations (in VS) above 2.9 g L-1 caused a lag phase of 5 days on biohydrogen production. No lag phase was observed for GW concentrations up to 25.6 g L-1. In the co-fermentation experiments, the highest hydrogen yield (46 ± 1 L kg-1) was achieved for GW:FW 90:10% (w/w). In the second stage, a biomethane yield of 682 ± 14 L kg-1 was obtained using the end-products of GW:FW 90:10% co-fermentation. The energy generation predictable from co-fermentation and AD of GW:FW 90:10% is 0.5 MJ kg-1 and 24.4 MJ kg-1, respectively, which represents an interesting alternative for valorisation of wastes produced locally in communities.
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Affiliation(s)
- A A Abreu
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - F Tavares
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - M M Alves
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.
| | - A J Cavaleiro
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.
| | - M A Pereira
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.
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Carlucci C, Jones CS, Oliphant K, Yen S, Daigneault M, Carriero C, Robinson A, Petrof EO, Weese JS, Allen-Vercoe E. Effects of defined gut microbial ecosystem components on virulence determinants of Clostridioides difficile. Sci Rep 2019; 9:885. [PMID: 30696914 PMCID: PMC6351598 DOI: 10.1038/s41598-018-37547-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 11/28/2018] [Indexed: 12/19/2022] Open
Abstract
Many cases of Clostridioides difficile infection (CDI) are poorly responsive to standard antibiotic treatment strategies, and often patients suffer from recurrent infections characterized by severe diarrhea. Our group previously reported the successful cure of two patients with recurrent CDI using a standardized stool-derived microbial ecosystem therapeutic (MET-1). Using an in vitro model of the distal gut to support bacterial communities, we characterized the metabolite profiles of two defined microbial ecosystems derived from healthy donor stool (DEC58, and a subset community, MET-1), as well as an ecosystem representative of a dysbiotic state (ciprofloxacin-treated DEC58). The growth and virulence determinants of two C. difficile strains were then assessed in response to components derived from the ecosystems. CD186 (ribotype 027) and CD973 (ribotype 078) growth was decreased upon treatment with DEC58 metabolites compared to ciprofloxacin-treated DEC58 metabolites. Furthermore, CD186 TcdA and TcdB secretion was increased following treatment with ciprofloxacin-treated DEC58 spent medium compared to DEC58 spent medium alone. The net metabolic output of C. difficile was also modulated in response to spent media from defined microbial ecosystems, although several metabolite levels were divergent across the two strains examined. Further investigation of these antagonistic properties will guide the development of microbiota-based therapeutics for CDI.
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Affiliation(s)
- Christian Carlucci
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
| | - Carys S Jones
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Kaitlyn Oliphant
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Sandi Yen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Michelle Daigneault
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Charley Carriero
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Avery Robinson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Elaine O Petrof
- Division of Infectious Diseases/Gastrointestinal Diseases Research Unit, Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - J Scott Weese
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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Coello K, Hansen TH, Sørensen N, Munkholm K, Kessing LV, Pedersen O, Vinberg M. Gut microbiota composition in patients with newly diagnosed bipolar disorder and their unaffected first-degree relatives. Brain Behav Immun 2019; 75:112-118. [PMID: 30261302 DOI: 10.1016/j.bbi.2018.09.026] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 08/23/2018] [Accepted: 09/24/2018] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVE An aberrant gut microbiota may be associated with a broad spectrum of diseases including mental illness. The gut microbiota is scarcely studied in bipolar disorder (BD). We examined the gut microbiota composition in patients with newly diagnosed BD, their unaffected first-degree relatives and healthy individuals. METHODS Stool samples were collected from 113 patients with BD, 39 unaffected first-degree relatives and 77 healthy individuals and the microbiota was profiled using 16S rRNA gene amplicon sequencing. RESULTS The gut microbiota community membership of patients with BD differed from that of healthy individuals (R2 = 1.0%, P = 0.008), whereas the community membership of unaffected first-degree relatives did not. Flavonifractor was present in 61% of patients with BD, 42% of their unaffected relatives and 39% of healthy individuals. Presence of Flavonifractor was associated with an odds ratio of 2.9 (95%CI: 1.6-5.2, P = 5.8 × 10-4, Q = 0.036) for having BD. When excluding smokers, presence of Flavonifractor was associated with an odds ratio of 2.3 (95%CI: 1.1-5.3, P = 0.019) for having BD. However, when considering the subsample of non-smokers only, BD and presence of Flavonifractor were no longer associated when adjusted for all possible tests at genus level (Q = 0.6). Presence of Flavonifractor in patients with BD was associated with smoking and female sex, but not with age, waist circumference, exercise level, high-sensitive C-reactive protein, current affective state, subtype of BD, illness duration or psychotropic medication, respectively. CONCLUSION Flavonifractor, a bacterial genus that may induce oxidative stress and inflammation in its host, was associated with BD. Higher prevalence of smoking among patients with BD contributed to our findings, and it cannot be excluded that findings are influenced by residual confounding.
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Affiliation(s)
- Klara Coello
- Copenhagen Affective Disorders Research Centre (CADIC), Psychiatric Center Copenhagen, Rigshospitalet, and Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
| | - Tue Haldor Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | | | - Klaus Munkholm
- Copenhagen Affective Disorders Research Centre (CADIC), Psychiatric Center Copenhagen, Rigshospitalet, and Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Lars Vedel Kessing
- Copenhagen Affective Disorders Research Centre (CADIC), Psychiatric Center Copenhagen, Rigshospitalet, and Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Maj Vinberg
- Copenhagen Affective Disorders Research Centre (CADIC), Psychiatric Center Copenhagen, Rigshospitalet, and Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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Solano-Aguilar GI, Jang S, Lakshman S, Gupta R, Beshah E, Sikaroodi M, Vinyard B, Molokin A, Gillevet PM, Urban JF. The Effect of Dietary Mushroom Agaricus bisporus on Intestinal Microbiota Composition and Host Immunological Function. Nutrients 2018; 10:nu10111721. [PMID: 30424006 PMCID: PMC6266512 DOI: 10.3390/nu10111721] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/28/2018] [Accepted: 11/02/2018] [Indexed: 12/11/2022] Open
Abstract
A study was designed to determine the potential prebiotic effect of dietary mushrooms on the host immune response, and intestinal microbiota composition and function. Thirty-one six-week-old pigs were fed a pig grower diet alone or supplemented with either three or six servings of freeze-dried white button (WB)-mushrooms for six weeks. Host immune response was evaluated in peripheral blood mononuclear cells (PBMC), and alveolar macrophages (AM) after stimulation with Salmonella typhymurium-Lipopolysaccharide (LPS). Isolated DNA from fecal and proximal colon contents were used for 16S rDNA taxonomic analysis and linear discriminant analysis effect size (LEfSe) to determine bacterial abundance and metabolic function. Pigs gained weight with no difference in body composition or intestinal permeability. Feeding mushrooms reduced LPS-induced IL-1β gene expression in AM (P < 0.05) with no change in LPS-stimulated PBMC or the intestinal mucosa transcriptome. LEfSe indicated increases in Lachnospiraceae, Ruminococcaceae within the order Clostridiales with a shift in bacterial carbohydrate metabolism and biosynthesis of secondary metabolites in the mushroom-fed pigs. These results suggested that feeding WB mushrooms significantly reduced the LPS-induced inflammatory response in AM and positively modulated the host microbiota metabolism by increasing the abundance of Clostridiales taxa that are associated with improved intestinal health.
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Affiliation(s)
- Gloria I Solano-Aguilar
- Diet Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture Northeast Area, Beltsville, MD 20705, USA.
| | - Saebyeol Jang
- Diet Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture Northeast Area, Beltsville, MD 20705, USA.
| | - Sukla Lakshman
- Diet Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture Northeast Area, Beltsville, MD 20705, USA.
| | - Richi Gupta
- Microbiome Analysis Center, George Mason University, Science & Technology Campus, Manassas, VA 20108, USA.
| | - Ethiopia Beshah
- Diet Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture Northeast Area, Beltsville, MD 20705, USA.
| | - Masoumeh Sikaroodi
- Microbiome Analysis Center, George Mason University, Science & Technology Campus, Manassas, VA 20108, USA.
| | - Bryan Vinyard
- Statistics Group, Agricultural Research Service, U.S. Department of Agriculture Northeast Area, Beltsville, MD 20705, USA.
| | - Aleksey Molokin
- Diet Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture Northeast Area, Beltsville, MD 20705, USA.
| | - Patrick M Gillevet
- Microbiome Analysis Center, George Mason University, Science & Technology Campus, Manassas, VA 20108, USA.
| | - Joseph F Urban
- Diet Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture Northeast Area, Beltsville, MD 20705, USA.
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Orf GS, Gisriel C, Redding KE. Evolution of photosynthetic reaction centers: insights from the structure of the heliobacterial reaction center. Photosynth Res 2018; 138:11-37. [PMID: 29603081 DOI: 10.1007/s11120-018-0503-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 03/22/2018] [Indexed: 05/24/2023]
Abstract
The proliferation of phototrophy within early-branching prokaryotes represented a significant step forward in metabolic evolution. All available evidence supports the hypothesis that the photosynthetic reaction center (RC)-the pigment-protein complex in which electromagnetic energy (i.e., photons of visible or near-infrared light) is converted to chemical energy usable by an organism-arose once in Earth's history. This event took place over 3 billion years ago and the basic architecture of the RC has diversified into the distinct versions that now exist. Using our recent 2.2-Å X-ray crystal structure of the homodimeric photosynthetic RC from heliobacteria, we have performed a robust comparison of all known RC types with available structural data. These comparisons have allowed us to generate hypotheses about structural and functional aspects of the common ancestors of extant RCs and to expand upon existing evolutionary schemes. Since the heliobacterial RC is homodimeric and loosely binds (and reduces) quinones, we support the view that it retains more ancestral features than its homologs from other groups. In the evolutionary scenario we propose, the ancestral RC predating the division between Type I and Type II RCs was homodimeric, loosely bound two mobile quinones, and performed an inefficient disproportionation reaction to reduce quinone to quinol. The changes leading to the diversification into Type I and Type II RCs were separate responses to the need to optimize this reaction: the Type I lineage added a [4Fe-4S] cluster to facilitate double reduction of a quinone, while the Type II lineage heterodimerized and specialized the two cofactor branches, fixing the quinone in the QA site. After the Type I/II split, an ancestor to photosystem I fixed its quinone sites and then heterodimerized to bind PsaC as a new subunit, as responses to rising O2 after the appearance of the oxygen-evolving complex in an ancestor of photosystem II. These pivotal events thus gave rise to the diversity that we observe today.
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Affiliation(s)
- Gregory S Orf
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, AZ, 85287, USA
| | - Christopher Gisriel
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, AZ, 85287, USA
- The Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287, USA
| | - Kevin E Redding
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
- Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, AZ, 85287, USA.
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Rosa BA, Supali T, Gankpala L, Djuardi Y, Sartono E, Zhou Y, Fischer K, Martin J, Tyagi R, Bolay FK, Fischer PU, Yazdanbakhsh M, Mitreva M. Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia. Microbiome 2018; 6:33. [PMID: 29486796 PMCID: PMC6389212 DOI: 10.1186/s40168-018-0416-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 01/26/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND The human intestine and its microbiota is the most common infection site for soil-transmitted helminths (STHs), which affect the well-being of ~ 1.5 billion people worldwide. The complex cross-kingdom interactions are not well understood. RESULTS A cross-sectional analysis identified conserved microbial signatures positively or negatively associated with STH infections across Liberia and Indonesia, and longitudinal samples analysis from a double-blind randomized trial showed that the gut microbiota responds to deworming but does not transition closer to the uninfected state. The microbiomes of individuals able to self-clear the infection had more alike microbiome assemblages compared to individuals who remained infected. One bacterial taxon (Lachnospiracae) was negatively associated with infection in both countries, and 12 bacterial taxa were significantly associated with STH infection in both countries, including Olsenella (associated with reduced gut inflammation), which also significantly reduced in abundance following clearance of infection. Microbial community gene abundances were also affected by deworming. Functional categories identified as associated with STH infection included arachidonic acid metabolism; arachidonic acid is the precursor for pro-inflammatory leukotrienes that threaten helminth survival, and our findings suggest that some modulation of arachidonic acid activity in the STH-infected gut may occur through the increase of arachidonic acid metabolizing bacteria. CONCLUSIONS For the first time, we identify specific members of the gut microbiome that discriminate between moderately/heavily STH-infected and non-infected states across very diverse geographical regions using two different statistical methods. We also identify microbiome-encoded biological functions associated with the STH infections, which are associated potentially with STH survival strategies, and changes in the host environment. These results provide a novel insight of the cross-kingdom interactions in the human gut ecosystem by unlocking the microbiome assemblages at taxonomic, genetic, and functional levels so that advances towards key mechanistic studies can be made.
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Affiliation(s)
- Bruce A. Rosa
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108 USA
| | - Taniawati Supali
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Lincoln Gankpala
- Public Health and Medical Research, National Public Health Institute of Liberia, Charlesville, Liberia
| | - Yenny Djuardi
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Erliyani Sartono
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Yanjiao Zhou
- Microbial Genomics, The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - Kerstin Fischer
- Department of Medicine, Washington University School of Medicine, St. Louis, MO USA
| | - John Martin
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108 USA
| | - Rahul Tyagi
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108 USA
| | - Fatorma K. Bolay
- Public Health and Medical Research, National Public Health Institute of Liberia, Charlesville, Liberia
| | - Peter U. Fischer
- Department of Medicine, Washington University School of Medicine, St. Louis, MO USA
| | - Maria Yazdanbakhsh
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Makedonka Mitreva
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108 USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO USA
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Freedman AJ, Tan B, Thompson JR. Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir. Environ Microbiol 2017; 19:2228-2245. [PMID: 28229521 PMCID: PMC5518199 DOI: 10.1111/1462-2920.13706] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 02/17/2017] [Indexed: 11/30/2022]
Abstract
Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO2 , harbor a 'deep carbonated biosphere' with carbon cycling potential. We sampled subsurface fluids from scCO2 -water separators at a natural scCO2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO2 and N2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO2 reservoir indicates that potential impacts of the deep biosphere on CO2 fate and transport should be taken into consideration as a component of GCS planning and modelling.
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Affiliation(s)
- Adam J.E. Freedman
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - BoonFei Tan
- Center for Environmental Sensing and ModelingSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Janelle R. Thompson
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Center for Environmental Sensing and ModelingSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
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Zhang S, Liu M, Chen Y, Pan YT. Achieving ethanol-type fermentation for hydrogen production in a granular sludge system by aeration. Bioresour Technol 2017; 224:349-357. [PMID: 27916500 DOI: 10.1016/j.biortech.2016.11.096] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 11/19/2016] [Accepted: 11/23/2016] [Indexed: 06/06/2023]
Abstract
To investigate the effects of aeration on hydrogen-producing granular system, experiments were performed in two laboratory-scale anaerobic internal circulation hydrogen production (AICHP) reactors. The preliminary experiment of Reactor 1 showed that direct aeration was beneficial to enhancing hydrogen production. After the direct aeration was implied in Reactor 2, hydrogen production rate (HPR) and hydrogen content were increased by 100% and 60%, respectively. In addition, mixed-acid fermentation was transformed into typical ethanol-type fermentation (ETF). Illumina MiSeq sequencing shows that the direct aeration did not change the species of hydrogen-producing bacteria but altered their abundance. Hydrogen-producing bacteria and ethanol-type fermentative bacteria were increased by 24.5% and 146.3%, respectively. Ethanoligenens sp. sharply increased by 162.2% and turned into predominant bacteria in the system. These findings indicated that appropriate direct aeration might be a novel and promising way to obtain ETF and enhance hydrogen production in practical use.
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Affiliation(s)
- Song Zhang
- College of Architecture and Environment, Sichuan University, Chengdu 610065, China
| | - Min Liu
- College of Architecture and Environment, Sichuan University, Chengdu 610065, China
| | - Ying Chen
- College of Architecture and Environment, Sichuan University, Chengdu 610065, China.
| | - Yu-Ting Pan
- College of Architecture and Environment, Sichuan University, Chengdu 610065, China
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Brás JLA, Pinheiro BA, Cameron K, Cuskin F, Viegas A, Najmudin S, Bule P, Pires VMR, Romão MJ, Bayer EA, Spencer HL, Smith S, Gilbert HJ, Alves VD, Carvalho AL, Fontes CMGA. Diverse specificity of cellulosome attachment to the bacterial cell surface. Sci Rep 2016; 6:38292. [PMID: 27924829 PMCID: PMC5141474 DOI: 10.1038/srep38292] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/07/2016] [Indexed: 12/02/2022] Open
Abstract
During the course of evolution, the cellulosome, one of Nature's most intricate multi-enzyme complexes, has been continuously fine-tuned to efficiently deconstruct recalcitrant carbohydrates. To facilitate the uptake of released sugars, anaerobic bacteria use highly ordered protein-protein interactions to recruit these nanomachines to the cell surface. Dockerin modules located within a non-catalytic macromolecular scaffold, whose primary role is to assemble cellulosomal enzymatic subunits, bind cohesin modules of cell envelope proteins, thereby anchoring the cellulosome onto the bacterial cell. Here we have elucidated the unique molecular mechanisms used by anaerobic bacteria for cellulosome cellular attachment. The structure and biochemical analysis of five cohesin-dockerin complexes revealed that cell surface dockerins contain two cohesin-binding interfaces, which can present different or identical specificities. In contrast to the current static model, we propose that dockerins utilize multivalent modes of cohesin recognition to recruit cellulosomes to the cell surface, a mechanism that maximises substrate access while facilitating complex assembly.
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Affiliation(s)
- Joana L. A. Brás
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
- NZYTech Genes & Enzymes, Campus do Lumiar, Estrada do Paço do Lumiar, Edifício E, r/c, 1649-038 Lisboa, Portugal
| | - Benedita A. Pinheiro
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Kate Cameron
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
| | - Fiona Cuskin
- Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Aldino Viegas
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Institute of Physical Biology, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Shabir Najmudin
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
| | - Pedro Bule
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
| | - Virginia M. R. Pires
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
| | - Maria João Romão
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Edward A. Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Holly L. Spencer
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Steven Smith
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Harry J. Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Victor D. Alves
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
| | - Ana Luísa Carvalho
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Carlos M. G. A. Fontes
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
- NZYTech Genes & Enzymes, Campus do Lumiar, Estrada do Paço do Lumiar, Edifício E, r/c, 1649-038 Lisboa, Portugal
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Bui TPN, Shetty SA, Lagkouvardos I, Ritari J, Chamlagain B, Douillard FP, Paulin L, Piironen V, Clavel T, Plugge CM, de Vos WM. Comparative genomics and physiology of the butyrate-producing bacterium Intestinimonas butyriciproducens. Environ Microbiol Rep 2016; 8:1024-1037. [PMID: 27717172 DOI: 10.1111/1758-2229.12483] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 09/14/2016] [Accepted: 09/29/2016] [Indexed: 05/21/2023]
Abstract
Intestinimonas is a newly described bacterial genus with representative strains present in the intestinal tract of human and other animals. Despite unique metabolic features including the production of butyrate from both sugars and amino acids, there is to date no data on their diversity, ecology, and physiology. Using a comprehensive phylogenetic approach, Intestinimomas was found to include at least three species that colonize primarily the human and mouse intestine. We focused on the most common and cultivable species of the genus, Intestinimonas butyriciproducens, and performed detailed genomic and physiological comparison of strains SRB521T and AF211, isolated from the mouse and human gut respectively. The complete 3.3-Mb genomic sequences of both strains were highly similar with 98.8% average nucleotide identity, testifying to their assignment to one single species. However, thorough analysis revealed significant genomic rearrangements, variations in phage-derived sequences, and the presence of new CRISPR sequences in both strains. Moreover, strain AF211 appeared to be more efficient than strain SRB521T in the conversion of the sugars arabinose and galactose. In conclusion, this study provides genomic and physiological insight into Intestinimonas butyriciproducens, a prevalent butyrate-producing species, differentiating strains that originate from the mouse and human gut.
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Affiliation(s)
- Thi Phuong Nam Bui
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, Wageningen, WE, 6708, The Netherlands
| | - Sudarshan Anand Shetty
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, Wageningen, WE, 6708, The Netherlands
| | - Ilias Lagkouvardos
- Technische Universität München, ZIEL Institute for Food and Health, Freising, 85354, Germany
| | - Jarmo Ritari
- Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, Helsinki, 00014, Finland
| | - Bhawani Chamlagain
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland
| | - François P Douillard
- Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, Helsinki, 00014, Finland
| | - Lars Paulin
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Vieno Piironen
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland
| | - Thomas Clavel
- Technische Universität München, ZIEL Institute for Food and Health, Freising, 85354, Germany
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, Wageningen, WE, 6708, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, Wageningen, WE, 6708, The Netherlands
- Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, Helsinki, 00014, Finland
- RPU Immunobiology, Department of Bacteriology and Immunology, Faculty of Medicine University of Helsinki, Helsinki, 00014, Finland
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Zhang D, Fu X, Dai X, Chen Y, Dai L. A new biological process for short-chain fatty acid generation from waste activated sludge improved by Clostridiales enhancement. Environ Sci Pollut Res Int 2016; 23:23972-23982. [PMID: 27638799 DOI: 10.1007/s11356-016-7579-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 09/01/2016] [Indexed: 06/06/2023]
Abstract
Short-chain fatty acids (SCFAs), the carbon source of biological nutrient removal, can be produced by waste activated sludge (WAS) anaerobic fermentation. To get more SCFAs from sludge, most studies in literature focused on the mechanical process control or the structure of microbial community; little attention has been paid to the key microorganisms and their function related to SCFA generation. In this study, a different sludge pretreated method, i.e., pretreating sludge by proteinase K for 2 days followed by pretreating at pH 10 for 4 days, is reported, by which the proportion of Clostridiales was increased and SCFA generation was enhanced. First, the effects of different proteinase K concentrations and initial pH on sludge hydrolysis and SCFA generation were investigated. The optimal conditions showed the highest SCFA generation (352.91 mg COD per gram of volatile suspended solids), which was 2.89-fold of the blank (un-pretreated). Further, the new biological pretreatment process led to the conversion of other SCFAs to acetic acid. Acetic acid accounted for 60.8 % of total SCFAs with the new biological pretreatment process compared with 44.9 % in the blank test. Then, the investigation on the key microorganisms related to SCFA production with 16S rRNA gene clone library and fluorescence in situ hybridization (FISH) indicated that there were much greater active Clostridiales when SCFAs were generated with the proteinase K and pH 10 pretreated sludge. Further, the mechanisms for the optimal conditions significantly enhancing SCFA generation were investigated. It was found that pretreating sludge by proteinase K and pH 10 caused the greatest key enzyme activities, organic consumption, and inhibition of methane generation. Graphical abstract A new biological process for short-chain fatty acid generation from waste activated sludge improved by Clostridiales enhancement.
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Affiliation(s)
- Dong Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Xiang Fu
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Xiaohu Dai
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Lingling Dai
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
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Abreu AA, Tavares F, Alves MM, Pereira MA. Boosting dark fermentation with co-cultures of extreme thermophiles for biohythane production from garden waste. Bioresour Technol 2016; 219:132-138. [PMID: 27484669 DOI: 10.1016/j.biortech.2016.07.096] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 06/06/2023]
Abstract
Proof of principle of biohythane and potential energy production from garden waste (GW) is demonstrated in this study in a two-step process coupling dark fermentation and anaerobic digestion. The synergistic effect of using co-cultures of extreme thermophiles to intensify biohydrogen dark fermentation is demonstrated using xylose, cellobiose and GW. Co-culture of Caldicellulosiruptor saccharolyticus and Thermotoga maritima showed higher hydrogen production yields from xylose (2.7±0.1molmol(-1) total sugar) and cellobiose (4.8±0.3molmol(-1) total sugar) compared to individual cultures. Co-culture of extreme thermophiles C. saccharolyticus and Caldicellulosiruptor bescii increased synergistically the hydrogen production yield from GW (98.3±6.9Lkg(-1) (VS)) compared to individual cultures and co-culture of T. maritima and C. saccharolyticus. The biochemical methane potential of the fermentation end-products was 322±10Lkg(-1) (CODt). Biohythane, a biogas enriched with 15% hydrogen could be obtained from GW, yielding a potential energy generation of 22.2MJkg(-1) (VS).
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Affiliation(s)
- Angela A Abreu
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Fábio Tavares
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Maria Madalena Alves
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Maria Alcina Pereira
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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Saminathan M, Sieo CC, Gan HM, Ravi S, Venkatachalam K, Abdullah N, Wong CMVL, Ho YW. Modulatory effects of condensed tannin fractions of different molecular weights from a Leucaena leucocephala hybrid on the bovine rumen bacterial community in vitro. J Sci Food Agric 2016; 96:4565-4574. [PMID: 26910767 DOI: 10.1002/jsfa.7674] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 02/15/2016] [Accepted: 02/15/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND Condensed tannin (CT) fractions of different molecular weights (MWs) may affect rumen microbial metabolism by altering bacterial diversity. In this study the effects of unfractionated CTs (F0) and five CT fractions (F1-F5) of different MWs (F1, 1265.8 Da; F2, 1028.6 Da; F3, 652.2 Da; F4, 562.2 Da; F5, 469.6 Da) from Leucaena leucocephala hybrid-Rendang (LLR) on the structure and diversity of the rumen bacterial community were investigated in vitro. RESULTS Real-time polymerase chain reaction assay showed that the total bacterial population was not significantly (P > 0.05) different among the dietary treatments. Inclusion of higher-MW CT fractions F1 and F2 significantly (P < 0.05) increased the Fibrobacter succinogenes population compared with F0 and CT fractions F3-F5. Although inclusion of F0 and CT fractions (F1-F5) significantly (P < 0.05) decreased the Ruminococcus flavefaciens population, there was no effect on the Ruminococcus albus population when compared with the control (without CTs). High-throughput sequencing of the V3 region of 16S rRNA showed that the relative abundance of genera Prevotella and unclassified Clostridiales was significantly (P < 0.05) decreased, corresponding with increasing MW of CT fractions, whereas cellulolytic bacteria of the genus Fibrobacter were significantly (P < 0.05) increased. Inclusion of higher-MW CT fractions F1 and/or F2 decreased the relative abundance of minor genera such as Ruminococcus, Streptococcus, Clostridium XIVa and Anaeroplasma but increased the relative abundance of Acinetobacter, Treponema, Selenomonas, Succiniclasticum and unclassified Spirochaetales compared with the control and lower-MW CT fractions. CONCLUSION This study indicates that CT fractions of different MWs may play an important role in altering the structure and diversity of the rumen bacterial community in vitro, and the impact was more pronounced for CT fractions with higher MW. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Mookiah Saminathan
- Institute of Bioscience, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Chin Chin Sieo
- Institute of Bioscience, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Han Ming Gan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
- Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Sharanya Ravi
- Institute of Bioscience, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Karthikkumar Venkatachalam
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Norhani Abdullah
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
- Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | | | - Yin Wan Ho
- Institute of Bioscience, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
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Ziganshin AM, Schmidt T, Lv Z, Liebetrau J, Richnow HH, Kleinsteuber S, Nikolausz M. Reduction of the hydraulic retention time at constant high organic loading rate to reach the microbial limits of anaerobic digestion in various reactor systems. Bioresour Technol 2016; 217:62-71. [PMID: 26853042 DOI: 10.1016/j.biortech.2016.01.096] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 01/22/2016] [Accepted: 01/25/2016] [Indexed: 05/27/2023]
Abstract
The effects of hydraulic retention time (HRT) reduction at constant high organic loading rate on the activity of hydrogen-producing bacteria and methanogens were investigated in reactors digesting thin stillage. Stable isotope fingerprinting was additionally applied to assess methanogenic pathways. Based on hydA gene transcripts, Clostridiales was the most active hydrogen-producing order in continuous stirred tank reactor (CSTR), fixed-bed reactor (FBR) and anaerobic sequencing batch reactor (ASBR), but shorter HRT stimulated the activity of Spirochaetales. Further decreasing HRT diminished Spirochaetales activity in systems with biomass retention. Based on mcrA gene transcripts, Methanoculleus and Methanosarcina were the predominantly active in CSTR and ASBR, whereas Methanosaeta and Methanospirillum activity was more significant in stably performing FBR. Isotope values indicated the predominance of aceticlastic pathway in FBR. Interestingly, an increased activity of Methanosaeta was observed during shortening HRT in CSTR and ASBR despite high organic acids concentrations, what was supported by stable isotope data.
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Affiliation(s)
- Ayrat M Ziganshin
- Department of Microbiology, Kazan (Volga Region) Federal University, Kazan 420008, The Republic of Tatarstan, Russia
| | - Thomas Schmidt
- Department of Biochemical Conversion, Deutsches Biomasseforschungszentrum gGmbH, 04347 Leipzig, Germany; Faculty of Agricultural and Environmental Sciences, University of Rostock, 18059 Rostock, Germany
| | - Zuopeng Lv
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Jan Liebetrau
- Department of Biochemical Conversion, Deutsches Biomasseforschungszentrum gGmbH, 04347 Leipzig, Germany
| | - Hans Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Marcell Nikolausz
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany.
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Sulfate Reduction and Inorganic Carbon Assimilation in Acidic Thermal Springs of the Kamchatka Peninsula. Mikrobiologiia 2016; 85:446-57. [PMID: 28853776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Thermoacidophilic sulfate reduction remains a poorly studied process, which was investigated in the present work. Radioisotope analysis with 35S-Iabeled sulfate was used to determine the rates of dissimilatory sulfate reduction in acidic thermal springs of Kamchatka, Russia. Sulfate reduction rates were found to vary from 0.054 to 12.9 nmol S04/(cm3 day). The Neftyanaya ploshchadka spring (Uzon caldera, 60'C, pH 4.2) and Oreshek spring (Mutnovskii volcano, 91'C, pH 3.5) exhibited the highest activity of sulfate-reducing prokaryotes. Stable enrich- ment'cultures reducing sulfate at pH and temperature values close to'the environmental ones were obtained from these springs. Analysis of the 16S rRNA gene sequences revealed that'a chemolithoautotrophic bacterium Ther- modesufobium sp. 3127-1 was responsible for sulfate reduction in the enrichment from the Oil Site spring. A chemoorganoheterotrophic archaeon Vulcanisaeta sp. 3102-1 (phylum Crenarchaeota) was identified in the en- richment from Oreshek spring. Thus, dissimilatory sulfate reduction under thermoacidophilic conditions was demonstrated and the agents responsible for this process were revealed.
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Boltyanskaya YV, Kevbrin VV. Trophic Interactions of Proteolytic Bacteria Proteinivorax tanatarense in an Alkalinphilic Microbial Community. Mikrobiologiia 2016; 85:458-465. [PMID: 28853777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Lythic action of an anaerobic proteolytic bacterium Proteinivorax tanatarense on organisms with different cell wall types was studied. In the absence of photosynthetic oxygen release, this proteolytic was able to grow on intact biomass of cyanobacteria belonging to various systematic groups. Itis probably their usual saprotrophic-satellite responsible for the regulation of abundance of primary producers during the dark phase. Growth also occurred on the biomass of a nonphototrophic gram-negative microorganism-Halomonas campisalis, a common component of alkaliphilic. microbial communities: Comparative analysis of the interaction of the proteolytic with.H. campisalis cells at different physiological states revealed the lytic action to be re- stricted to dead and/or weakened cells, rather than the actively dividing ones. Strict specificity of the action of the proteolytic bacterium on gram-negative microorganisms with no effect on gram-positive ones was shown.
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Zhang M, Wang H, Han X. Preparation of metal-resistant immobilized sulfate reducing bacteria beads for acid mine drainage treatment. Chemosphere 2016; 154:215-223. [PMID: 27058913 DOI: 10.1016/j.chemosphere.2016.03.103] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 03/17/2016] [Accepted: 03/22/2016] [Indexed: 06/05/2023]
Abstract
Novel immobilized sulfate-reducing bacteria (SRB) beads were prepared for the treatment of synthetic acid mine drainage (AMD) containing high concentrations of Fe, Cu, Cd and Zn using up-flow anaerobic packed-bed bioreactor. The tolerance of immobilized SRB beads to heavy metals was significantly enhanced compared with that of suspended SRB. High removal efficiencies of sulfate (61-88%) and heavy metals (>99.9%) as well as slightly alkaline effluent pH (7.3-7.8) were achieved when the bioreactor was fed with acidic influent (pH 2.7) containing high concentrations of multiple metals (Fe 469 mg/L, Cu 88 mg/L, Cd 92 mg/L and Zn 128 mg/L), which showed that the bioreactor filled with immobilized SRB beads had tolerance to AMD containing high concentrations of heavy metals. Partially decomposed maize straw was a carbon source and stabilizing agent in the initial phase of bioreactor operation but later had to be supplemented by a soluble carbon source such as sodium lactate. The microbial community in the bioreactor was characterized by denaturing gradient gel electrophoresis (DGGE) and sequencing of partial 16S rDNA genes. Synergistic interaction between SRB (Desulfovibrio desulfuricans) and co-existing fermentative bacteria could be the key factor for the utilization of complex organic substrate (maize straw) as carbon and nutrients source for sulfate reduction.
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Affiliation(s)
- Mingliang Zhang
- School of Resources and Environment, University of Jinan, Jinan 250022, China.
| | - Haixia Wang
- School of Resources and Environment, University of Jinan, Jinan 250022, China
| | - Xuemei Han
- School of Resources and Environment, University of Jinan, Jinan 250022, China
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74
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Fisinin VI, Il'ina LA, Iyldyrym EA, Nikonov IN, Filippova VA, Laptev GY, Novikova NI, Grozina AA, Lenkova TN, Manukya VA, Egorov IA. Broiler Cecal Microbiocenoses Depending on Mixed Fodder. Mikrobiologiia 2016; 85:472-480. [PMID: 28853779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Molecular genetic techniques (NGS sequencing and quantitative PCR) were used to determine the composition of the cecal bacterial community of broiler chickens fed with different mixed fodder. The Cecal microbiome exhibited taxonomic diversity, with both typical inhabitants of avian intestine belonging to the families Clostridiaceae, Eubacteriaceae, and Lactobacillaceae and to the phylum Bacteroidetes, and new un- identified taxa, as well as bacteria of the families Lachnospiraceae and Ruminococcaceae, which were previ- ously considered restricted to the rumen microflora. Contrary to traditional concepts, enterococci and bi- fidobacteria were among the minor components of the community, lactate-fermenting species were absent, and typical avian pathogens of the genus Staphylococcus were detected but seldom. Members of the family Suterellaceae and the genus Gallibacterium, which are responsible for avian respiratory infections, were also detected. Significant fluctuations of abundance and composition of microbial groups within the cecal com- munity and of the parameters of broiler productivity were found to occur depending on the feed allowance. Cellulose content in the feed had the most pronounced effect on the composition aid structure of bacterial communities. Decreased cellulose content resulted in a decrease of bacterial abundance by-aii order of mag- nitude and in increased ratios of members of the phylum Bacteroidetes and the family Clostridiaceae, which possess the enzymes degrading starch polysadcharides. Abundance of the normal inhabitants of avian intes- tine belonging to the genus Ldctobacillus and the order Bacillales decreased, while the share of Escherichia and members of the family Sutterellaceae increased, including some species capable of causing dysbiotic changes in avian intestine. No significant change in abundance of cellulolytics of the families Ruminococca- ceae, Lachnospiraceae, and Eubacteriaceae was observed.
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Dai X, Yan H, Li N, He J, Ding Y, Dai L, Dong B. Metabolic adaptation of microbial communities to ammonium stress in a high solid anaerobic digester with dewatered sludge. Sci Rep 2016; 6:28193. [PMID: 27312792 PMCID: PMC4911566 DOI: 10.1038/srep28193] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/01/2016] [Indexed: 11/25/2022] Open
Abstract
A high solid digester with dewatered sludge was operated for 110 days to ascertain the interactions between bacterial and archaeal communities under ammonium stress, as well as the corresponding changes in bio-degradation mechanisms. The volatile solids reduction (95% confidence intervals in mean) changed from 31.6 ± 0.9% in the stable period (day 40-55) to 21.3 ± 1.5% in the last period (day 71-110) when ammonium concentration was elevated to be within 5,000-6,000 mgN/L. Biogas yield dropped accordingly from 11.9 ± 0.3 to 10.4 ± 0.2 L/d and carbon dioxide increased simultaneously from 35.2% to 44.8%. Anaerobranca better adapted to the ammonium stress, while the initially dominant protein-degrading microbes-Tepidimicrobium and Proteiniborus were suppressed, probably responsible for the increase of protein content in digestate. Meanwhile, Methanosarcina, as the dominant Archaea, was resistant to ammonium stress with the constant relative abundance of more than 92% during the whole operation. Nonmetric Multidimensional Scaling (NMDS) analysis was thus conducted which indicated that the gradually increased TAN dictated the bacterial clusters. The dominant Methanosarcina and the increased carbon dioxide content under ammonium stress suggested that, rather than the commonly acknowledged syntrophic acetate oxidation (SAO) with hydrogenotrophic methanogenesis, only SAO pathway was enhanced during the initial 'ammonium inhibition'.
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Affiliation(s)
- Xiaohu Dai
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
| | - Han Yan
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
| | - Ning Li
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
| | - Jin He
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
| | - Yueling Ding
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
| | - Lingling Dai
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
| | - Bin Dong
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
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Zhao C, Pyle AM. Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution. Nat Struct Mol Biol 2016; 23:558-65. [PMID: 27136328 PMCID: PMC4899126 DOI: 10.1038/nsmb.3224] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/06/2016] [Indexed: 12/17/2022]
Abstract
Group II introns are self-splicing ribozymes that are essential in many organisms, and they have been hypothesized to share a common evolutionary ancestor with the spliceosome. Although structural similarity of RNA components supports this connection, it is of interest to determine whether associated protein factors also share an evolutionary heritage. Here we present the crystal structures of reverse transcriptase (RT) domains from two group II intron-encoded proteins (maturases) from Roseburia intestinalis and Eubacterium rectale, obtained at 1.2-Å and 2.1-Å resolution, respectively. These domains are more similar in architecture to the spliceosomal Prp8 RT-like domain than to any other RTs, and they share substantial similarity with flaviviral RNA polymerases. The RT domain itself is sufficient for binding intron RNA with high affinity and specificity, and it is contained within an active RT enzyme. These studies provide a foundation for understanding structure-function relationships within group II intron-maturase complexes.
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Affiliation(s)
- Chen Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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Starke R, Keller A, Jehmlich N, Vogt C, Richnow HH, Kleinsteuber S, von Bergen M, Seifert J. Pulsed (13)C2-Acetate Protein-SIP Unveils Epsilonproteobacteria as Dominant Acetate Utilizers in a Sulfate-Reducing Microbial Community Mineralizing Benzene. Microb Ecol 2016; 71:901-11. [PMID: 26846217 DOI: 10.1007/s00248-016-0731-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/18/2016] [Indexed: 05/23/2023]
Abstract
In a benzene-degrading and sulfate-reducing syntrophic consortium, a clostridium affiliated to the genus Pelotomaculum was previously described to ferment benzene while various sulfate-reducing Deltaproteobacteria and a member of the Epsilonproteobacteria were supposed to utilize acetate and hydrogen as key metabolites derived from benzene fermentation. However, the acetate utilization network within this community was not yet unveiled. In this study, we performed a pulsed (13)C2-acetate protein stable isotope probing (protein-SIP) approach continuously spiking low amounts of acetate (10 μM per day) in addition to the ongoing mineralization of unlabeled benzene. Metaproteomics revealed high abundances of Clostridiales followed by Syntrophobacterales, Desulfobacterales, Desulfuromonadales, Desulfovibrionales, Archaeoglobales, and Campylobacterales. Pulsed acetate protein-SIP results indicated that members of the Campylobacterales, the Syntrophobacterales, the Archaeoglobales, the Clostridiales, and the Desulfobacterales were linked to acetate utilization in descending abundance. The Campylobacterales revealed the fastest and highest (13)C incorporation. Previous experiments suggested that the activity of the Campylobacterales was not essential for anaerobic benzene degradation in the investigated community. However, these organisms were consistently detected in various hydrocarbon-degrading and sulfate-reducing consortia enriched from the same aquifer. Here, we demonstrate that this member of the Campylobacterales is the dominant acetate utilizer in the benzene-degrading microbial consortium.
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Affiliation(s)
- Robert Starke
- Institute for Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70599, Stuttgart, Germany
- Department of Proteomics, Helmholtz-Centre for Environmental Research (UFZ), Permoserstr. 15, 04318, Leipzig, Germany
| | - Andreas Keller
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research (UFZ), Permoserstr. 15, 04318, Leipzig, Germany
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research (UFZ), Permoserstr. 15, 04318, Leipzig, Germany
| | - Nico Jehmlich
- Department of Proteomics, Helmholtz-Centre for Environmental Research (UFZ), Permoserstr. 15, 04318, Leipzig, Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research (UFZ), Permoserstr. 15, 04318, Leipzig, Germany
| | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research (UFZ), Permoserstr. 15, 04318, Leipzig, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research (UFZ), Permoserstr. 15, 04318, Leipzig, Germany
| | - Martin von Bergen
- Department of Proteomics, Helmholtz-Centre for Environmental Research (UFZ), Permoserstr. 15, 04318, Leipzig, Germany
- Department of Metabolomics, Helmholtz-Centre for Environmental Research (UFZ), Permoserstr. 15, 04318, Leipzig, Germany
| | - Jana Seifert
- Institute for Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70599, Stuttgart, Germany.
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Liu T, Ahn H, Sun W, McGuinness LR, Kerkhof LJ, Häggblom MM. Identification of a Ruminococcaceae Species as the Methyl tert-Butyl Ether (MTBE) Degrading Bacterium in a Methanogenic Consortium. Environ Sci Technol 2016; 50:1455-1464. [PMID: 26727046 DOI: 10.1021/acs.est.5b04731] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The widespread use of methyl tert-butyl ether (MTBE) has caused major contamination of groundwater sources and is a concern due to its taste and odor problems, as well as its toxicity. MTBE can be degraded anaerobically which makes bioremediation of contaminated aquifers a potential solution. Nevertheless, the organisms and mechanisms that are responsible for anaerobic MTBE degradation are still unknown. The aim of our research was to identify the organisms actively degrading MTBE. For this purpose we characterized an anaerobic methanogenic culture enriched with MTBE as the sole carbon source from the New Jersey Arthur Kill intertidal strait sediment. The cultures were analyzed using stable isotope probing (SIP) combined with terminal restriction fragment length polymorphism (T-RFLP), high-throughput sequencing and clone library analysis of bacterial 16S rRNA genes. The sequence data indicated that phylotypes belonging to the Ruminococcaceae in the Firmicutes were predominant in the methanogenic cultures. SIP experiments also showed sequential incorporation of the (13)C labeled MTBE by the bacterial community with a bacterium most closely related to Saccharofermentans acetigenes identified as the bacterium active in O-demethylation of MTBE. Identification of the microorganisms responsible for the activity will help us better understand anaerobic MTBE degradation processes in the field and determine biomarkers for monitoring natural attenuation.
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Affiliation(s)
- Tong Liu
- Department of Biochemistry and Microbiology, Rutgers University , New Brunswick, New Jersey 08901, United States
| | - Hyeri Ahn
- Department of Biochemistry and Microbiology, Rutgers University , New Brunswick, New Jersey 08901, United States
| | - Weimin Sun
- Department of Biochemistry and Microbiology, Rutgers University , New Brunswick, New Jersey 08901, United States
| | - Lora R McGuinness
- Department of Marine and Coastal Science, Rutgers University , New Brunswick, New Jersey 08901, United States
| | - Lee J Kerkhof
- Department of Marine and Coastal Science, Rutgers University , New Brunswick, New Jersey 08901, United States
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers University , New Brunswick, New Jersey 08901, United States
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Song H, Yoo Y, Hwang J, Na YC, Kim HS. Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis. J Allergy Clin Immunol 2015; 137:852-60. [PMID: 26431583 DOI: 10.1016/j.jaci.2015.08.021] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 07/20/2015] [Accepted: 08/12/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND Atopic dermatitis (AD) is a serious global epidemic associated with a modern lifestyle. OBJECTIVE Although aberrant interactions between gut microbes and the intestinal immune system have been implicated in this skin disease, the nature of the microbiome dysfunction underlying the disease remains unclear. METHODS The gut microbiome from 132 subjects, including 90 patients with AD, was analyzed by using 16S rRNA gene and metagenome sequence analyses. Reference genomes from the Human Microbiome Project and the KEGG Orthology database were used for metagenome analyses. Short-chain fatty acids in fecal samples were compared by using gas chromatographic-mass spectrometric analyses. RESULTS We show that enrichment of a subspecies of the major gut species Faecalibacterium prausnitzii is strongly associated with AD. In addition, the AD microbiome was enriched in genes encoding the use of various nutrients that could be released from damaged gut epithelium, reflecting a bloom of auxotrophic bacteria. Fecal samples from patients with AD showed decreased levels of butyrate and propionate, which have anti-inflammatory effects. This is likely a consequence of an intraspecies compositional change in F prausnitzii that reduces the number of high butyrate and propionate producers, including those related to the strain A2-165, a lack of which has been implicated in patients with Crohn disease. CONCLUSIONS The data suggest that feedback interactions between dysbiosis in F prausnitzii and dysregulation of gut epithelial inflammation might underlie the chronic progression of AD by resulting in impairment of the gut epithelial barrier, which ultimately leads to aberrant TH2-type immune responses to allergens in the skin.
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Affiliation(s)
- Han Song
- Department of Biomedical Sciences, Korea University, Seoul, Korea
| | - Young Yoo
- Department of Pediatrics, Korea University, Seoul, Korea
| | - Junghyun Hwang
- Department of Biomedical Sciences, Korea University, Seoul, Korea
| | - Yun-Cheol Na
- Western Seoul Center, Korea Basic Science Institute, Seoul, Korea
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80
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Yun J, Kim TG, Cho KS. Suppression of methanogenesis in hydrogen fermentation by intermittent feeding. J Environ Sci Health A Tox Hazard Subst Environ Eng 2015; 50:1458-1467. [PMID: 26325509 DOI: 10.1080/10934529.2015.1074480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This study investigated whether intermittent feeding by using a concentrated carbon source is an appropriate method for selective enrichment of hydrogenesis by means of methanogen suppression. In a conventional reactor fed continuously for 10 d, methanogens increased from 2.8 × 10(7) to 1.1 × 10(9) gene copy number (GCN)/mg-cell dry weight, and methane concentration in the resulting biogas was 5.8%. However, when a carbon source was intermittently supplied for 10 d to the reactor, the number of methanogens was reduced 98.9% from 2.77 × 10(7) to 1.2 × 10(3) GCN/mg-cell dry weight, and methane was not detected during this period of intermittent feeding. Intermittent feeding shifted the dominants in the reactor from Clostridiaceae (70.5%) and Lactobacillaceae (11.0%) to Acetobacteraceae (62.0%) and Clostridiaceae (38.0%). In the reactor operated in continuous feeding mode after intermittent feeding, methane concentration was below 0.3% and the portion of methanogens in the bacterial community was maintained below 0.2%. These results suggest that the intermittent feeding of a carbon source during hydrogen production processes is a suitable method to suppress the activity of methanogens.
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Affiliation(s)
- Jeonghee Yun
- a Department of Environmental Science and Engineering , Ewha Womans University , Seoul , South Korea
| | - Tae Gwan Kim
- a Department of Environmental Science and Engineering , Ewha Womans University , Seoul , South Korea
| | - Kyung-Suk Cho
- a Department of Environmental Science and Engineering , Ewha Womans University , Seoul , South Korea
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Barrios C, Beaumont M, Pallister T, Villar J, Goodrich JK, Clark A, Pascual J, Ley RE, Spector TD, Bell JT, Menni C. Gut-Microbiota-Metabolite Axis in Early Renal Function Decline. PLoS One 2015; 10:e0134311. [PMID: 26241311 PMCID: PMC4524635 DOI: 10.1371/journal.pone.0134311] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 07/07/2015] [Indexed: 01/15/2023] Open
Abstract
Introduction Several circulating metabolites derived from bacterial protein fermentation have been found to be inversely associated with renal function but the timing and disease severity is unclear. The aim of this study is to explore the relationship between indoxyl-sulfate, p-cresyl-sulfate, phenylacetylglutamine and gut-microbial profiles in early renal function decline. Results Indoxyl-sulfate (Beta(SE) = -2.74(0.24); P = 8.8x10-29), p-cresyl-sulfate (-1.99(0.24), P = 4.6x10-16), and phenylacetylglutamine(-2.73 (0.25), P = 1.2x10-25) were inversely associated with eGFR in a large population base cohort (TwinsUK, n = 4439) with minimal renal function decline. In a sub-sample of 855 individuals, we analysed metabolite associations with 16S gut microbiome profiles (909 profiles, QIIME 1.7.0). Three Operational Taxonomic Units (OTUs) were significantly associated with indoxyl-sulfate and 52 with phenylacetylglutamine after multiple testing; while one OTU was nominally associated with p-cresyl sulfate. All 56 microbial members belong to the order Clostridiales and are represented by anaerobic Gram-positive families Christensenellaceae, Ruminococcaceae and Lachnospiraceae. Within these, three microbes were also associated with eGFR. Conclusions Our data suggest that indoxyl-sulfate, p-cresyl-sulfate and phenylacetylglutamine are early markers of renal function decline. Changes in the intestinal flora associated with these metabolites are detectable in early kidney disease. Future efforts should dissect this relationship to improve early diagnostics and therapeutics strategies.
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Affiliation(s)
- Clara Barrios
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
- Department of Nephrology, Hospital del Mar, Institut Mar d’Investigacions Mediques, Barcelona, Spain
- * E-mail: (CB); (CM)
| | - Michelle Beaumont
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Tess Pallister
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Judith Villar
- Department of Infectious Diseases, Hospital del Mar, Institut Mar d’Investigacions Mediques, Barcelona, Spain
| | - Julia K. Goodrich
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States of America
| | - Andrew Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States of America
| | - Julio Pascual
- Department of Nephrology, Hospital del Mar, Institut Mar d’Investigacions Mediques, Barcelona, Spain
| | - Ruth E. Ley
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States of America
| | - Tim D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Jordana T. Bell
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
- * E-mail: (CB); (CM)
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Rodrigues MLM, Leão VA, Gomes O, Lambert F, Bastin D, Gaydardzhiev S. Copper extraction from coarsely ground printed circuit boards using moderate thermophilic bacteria in a rotating-drum reactor. Waste Manag 2015; 41:148-158. [PMID: 25899037 DOI: 10.1016/j.wasman.2015.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 03/26/2015] [Accepted: 04/01/2015] [Indexed: 06/04/2023]
Abstract
The current work reports on a new approach for copper bioleaching from Printed Circuit Board (PCB) by moderate thermophiles in a rotating-drum reactor. Initially leaching of PCB was carried out in shake flasks to assess the effects of particle size (-208μm+147μm), ferrous iron concentration (1.25-10.0g/L) and pH (1.5-2.5) on copper leaching using mesophile and moderate thermophile microorganisms. Only at a relatively low solid content (10.0g/L) complete copper extraction was achieved from the particle size investigated. Conversely, high copper extractions were possible from coarse-ground PCB (20mm-long) working with increased solids concentration (up to 25.0g/L). Because there was as the faster leaching kinetics at 50°C Sulfobacillus thermosulfidooxidans was selected for experiments in a rotating-drum reactor with the coarser-sized PCB sheets. Under optimal conditions, copper extraction reached 85%, in 8days and microscopic observations by SEM-EDS of the on non-leached and leached material suggested that metal dissolution from the internal layers was restricted by the fact that metal surface was not entirely available and accessible for the solution in the case of the 20mm-size sheets.
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Affiliation(s)
- Michael L M Rodrigues
- Bio&Hydrometallurgy Laboratory, Department of Metallurgical and Materials Engineering, Universidade Federal de Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, MG 35400-000, Brazil.
| | - Versiane A Leão
- Bio&Hydrometallurgy Laboratory, Department of Metallurgical and Materials Engineering, Universidade Federal de Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, MG 35400-000, Brazil.
| | - Otavio Gomes
- Centre for Mineral Technology - CETEM, Av Pedro Calmon, 900, 21941-908 Rio de Janeiro, Brazil
| | - Fanny Lambert
- Mineral Processing and Recycling, University of Liege, SartTilman, 4000 Liege, Belgium
| | - David Bastin
- Mineral Processing and Recycling, University of Liege, SartTilman, 4000 Liege, Belgium
| | - Stoyan Gaydardzhiev
- Mineral Processing and Recycling, University of Liege, SartTilman, 4000 Liege, Belgium
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Moshi AP, Hosea KMM, Elisante E, Mamo G, Mattiasson B. High temperature simultaneous saccharification and fermentation of starch from inedible wild cassava (Manihot glaziovii) to bioethanol using Caloramator boliviensis. Bioresour Technol 2015; 180:128-136. [PMID: 25594508 DOI: 10.1016/j.biortech.2014.12.087] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 12/23/2014] [Accepted: 12/24/2014] [Indexed: 06/04/2023]
Abstract
The thermoanaerobe, Caloramator boliviensis was used to ferment starch hydrolysate from inedible wild cassava to ethanol at 60°C. A raw starch degrading α-amylase was used to hydrolyse the cassava starch. During fermentation, the organism released CO2 and H2 gases, and Gas Endeavour System was successfully used for monitoring and recording formation of these gaseous products. The bioethanol produced in stoichiometric amounts to CO2 was registered online in Gas Endeavour software and correlated strongly (R(2)=0.99) with values measured by HPLC. The organism was sensitive to cyanide that exists in cassava flour. However, after acclimatisation, it was able to grow and ferment cassava starch hydrolysate containing up to 0.2ppm cyanide. The reactor hydrogen partial pressure had influence on the bioethanol production. In fed-batch fermentation by maintaining the hydrogen partial pressure around 590Pa, the organism was able to ferment up to 76g/L glucose and produced 33g/L ethanol.
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Affiliation(s)
- Anselm P Moshi
- Division of Biotechnology, Lund University, P.O. Box 124, SE-22100 Lund, Sweden; Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, Uvumbuzi Road, Mwalimu J.K. Nyerere Mlimani Campus, University of Dar es Salaam, P.O. Box 35179, Dar es Salaam, Tanzania; Tanzania Industrial Research and Development Organization (TIRDO), Kimweri Avenue, TIRDO Complex, Msasani, P.O. Box 23235, Dar-es salaam, Tanzania.
| | - Ken M M Hosea
- Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, Uvumbuzi Road, Mwalimu J.K. Nyerere Mlimani Campus, University of Dar es Salaam, P.O. Box 35179, Dar es Salaam, Tanzania.
| | - Emrode Elisante
- Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, Uvumbuzi Road, Mwalimu J.K. Nyerere Mlimani Campus, University of Dar es Salaam, P.O. Box 35179, Dar es Salaam, Tanzania.
| | - G Mamo
- Division of Biotechnology, Lund University, P.O. Box 124, SE-22100 Lund, Sweden.
| | - Bo Mattiasson
- Division of Biotechnology, Lund University, P.O. Box 124, SE-22100 Lund, Sweden; also at Indienz AB, Annebergs Gård, SE-26873 Billeberga, Sweden.
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