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Mang Q, Gao J, Li Q, Sun Y, Xu G, Xu P. Integrative analysis of metagenome and metabolome provides new insights into intestinal health protection in Coilia nasus larvae via probiotic intervention. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101230. [PMID: 38643745 DOI: 10.1016/j.cbd.2024.101230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/20/2024] [Accepted: 03/29/2024] [Indexed: 04/23/2024]
Abstract
With the development of large-scale intensive feeding, growth performance and animal welfare have attracted more and more attention. Exogenous probiotics can promote the growth performance of fish through improving intestinal microbiota; however, it remains unclear whether intestinal microbiota influence physiological biomarkers. Therefore, we performed metagenomic and metabolomic analysis to investigate the effects of a 90-day Lactiplantibacillus plantarum supplementation to a basal diet (1.0 × 108 CFU/g) on the growth performance, intestinal microbiota and their metabolites, and physiological biomarkers in Coilia nasus larvae. The results showed that the probiotic supplementation could significantly increase weight and body length. Moreover, it could also enhance digestive enzymes and tight junctions, and inhibit oxidative stress and inflammation. The metagenomic analysis showed that L. plantarum supplementation could significantly decrease the relative abundance of Proteobacteria and increase the relative abundance of Firmicutes. Additionally, pathogenic bacteria (Aeromonadaceae, Aeromonas, and Enterobacterales) were inhibited and beneficial bacteria (Bacillales) were promoted. The metabolome analysis showed that acetic acid and propanoic acid were significantly elevated, and were associated with Kitasatospora, Seonamhaeicola, and Thauera. A correlation analysis demonstrated that the digestive enzymes, tight junction, oxidative stress, and inflammation effects were significantly associated with the increased acetic acid and propanoic acid levels. These results indicated that L. plantarum supplementation could improve intestinal microbial community structure and function, which could raise acetic acid and propanoic acid levels to protect intestinal health and improve growth performance in C. nasus larvae.
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Affiliation(s)
- Qi Mang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Jun Gao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Quanjie Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Yi Sun
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Gangchun Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China.
| | - Pao Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China.
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González M, Cerda Á, Rodríguez C, Serrano J, Leiva E. Coupling of the Feammox - Anammox pathways by using a sequential discontinuous bioreactor. BIORESOURCE TECHNOLOGY 2024; 395:130334. [PMID: 38242238 DOI: 10.1016/j.biortech.2024.130334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/11/2024] [Accepted: 01/13/2024] [Indexed: 01/21/2024]
Abstract
Treating nitrogenous compounds in wastewater is a contemporary challenge, prompting novel approaches for ammonium (NH4+) conversion to molecular nitrogen (N2). This study explores the classic anaerobic ammonium oxidation process (Anammox) coupled to the iron-dependent anaerobic ammonium oxidation process (Feammox) in a sequential discontinuous bioreactor (SBR) for NH4+ removal. Feammox and Anammox cultures were individually enriched and combined, optimizing the coupling, and identifying key variables influencing the enrichment process. Adding sodium acetate as a carbon source significantly reduces Fe3+ to Fe2+, indicating Feammox activity. Both Anammox and Feammox processes were successfully operated in SBRs, achieving efficient NH4+ removal (Anammox: 64.6 %; Feammox: 43.4 %). Combining these pathways in a single SBR enhances the NH4+ removal capacity of 50.8 %, improving Feammox efficiency. The Feammox process coupled with Anammox may generate the nitrite (NO2-) needed for Anammox. This research contributes to biotechnological advancements for sustainable nitrogenous compound treatment in SBRs.
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Affiliation(s)
- Macarena González
- Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul 7820436, Santiago, Chile
| | - Ámbar Cerda
- Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul 7820436, Santiago, Chile.
| | - Carolina Rodríguez
- Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul 7820436, Santiago, Chile.
| | - Jennyfer Serrano
- Escuela de Biotecnología, Universidad Mayor, Camino La Pirámide 5750, Huechuraba, Santiago 8580745, Chile.
| | - Eduardo Leiva
- Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul 7820436, Santiago, Chile; Departamento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, 7820436, Santiago, Chile.
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Im S, Kang S, Jang D, Kim G, Kim DH. Use of reverse osmosis concentrate for mitigating greenhouse gas emissions from pig slurry. Front Microbiol 2023; 14:1180018. [PMID: 37266025 PMCID: PMC10229891 DOI: 10.3389/fmicb.2023.1180018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 04/24/2023] [Indexed: 06/03/2023] Open
Abstract
Due to the high global warming potential (GWP) in a short time scale (GWP100 = 28 vs. GWP20 = 86), mitigating CH4 emissions could have an early impact on reducing current global warming effects. The manure storage tank emits a significant amount of CH4, which can diminish the environmental benefit resulting from the anaerobic digestion of manure that can generate renewable energy. In the present study, we added the reverse osmosis concentrate (ROC) rich in salt to the pig slurry (PS) storage tank to reduce CH4 emissions. Simultaneously, pure NaCl was tested at the same concentration to compare and verify the performance of ROC addition. During 40 days of storage, 1.83 kg CH4/ton PS was emitted, which was reduced by 7-75% by the addition of ROC at 1-9 g Na+/L. This decrease was found to be more intensive than that found upon adding pure sodium, which was caused by the presence of sulfate rich in ROC, resulting in synergistic inhibition. The results of the microbial community and activity test showed that sodium directly inhibited methanogenic activity rather than acidogenic activity. In the subsequent biogas production from the stored PS, more CH4 was obtained by ROC addition due to the preservation of organic matter during storage. Overall, 51.2 kg CO2 eq./ton PS was emitted during the storage, while 8 kg CO2 eq./ton PS was reduced by biogas production in the case of control, resulting in a total of 43.2 kg CO2 eq./ton PS. This amount of greenhouse gas emissions was reduced by ROC addition at 5 g Na+/L by 22 and 65 kg CO2 eq./ton PS, considering GWP100 and GWP20 of CH4, respectively, where most of the reduction was achieved during the storage process. To the best of our knowledge, this was the first report using salty waste to reduce GHG emissions in a proper place, e.g., a manure storage tank.
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Affiliation(s)
- Seongwon Im
- Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Sungwon Kang
- Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Duksoo Jang
- Department of Global Smart City, Sungkyunkwan University (SKKU), Suwon-si, Gyeonggi-do, Republic of Korea
| | - Gyeongchul Kim
- Department of Civil Engineering, Inha University, Incheon, Republic of Korea
| | - Dong-Hoon Kim
- Department of Civil Engineering, Inha University, Incheon, Republic of Korea
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Xing BS, Tang XF, Wang R, Cao S, Wen J, Zhang Y, Chang XL, Wang XC, Chen R. Comparative study of the effect of loading increments on the mesophilic codigestion of waste activated sludge and food waste: Reactor performance, stability analysis, and microbial community. CHEMOSPHERE 2022; 308:136308. [PMID: 36067815 DOI: 10.1016/j.chemosphere.2022.136308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/24/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
The performance and stability of mesophilic codigestion of waste activated sludge (WAS) and food waste (FW) were compared in two parallel, continuously stirred tank reactors using high- and low-magnitude loading increments for the loading regimes. The results indicated that a high methane (CH4) production of 6.98 L L-1·d-1 was realized without volatile fatty acid accumulation via low-magnitude loading increments at a high loading of 26.5 g-COD·L-1·d-1, and this system was more stable and achieved a higher efficiency than the codigestion system that used high-magnitude loading increments at similar loading and operating conditions. Furthermore, higher CH4 yields of 258-334 mL-CH4·g-COD-1, TCOD removal efficiencies of 64-79%, conversion ratios of 62-88%, and methanogenic activities of 0.37-0.40 g-CH4-COD·g-VS-1·d-1 were consistently maintained via the low-magnitude loading increments during the high-rate period. High abundances of the phyla Firmicutes (63.3%) and genus Methanosarcina (94.5%) contributed to the high rates and stable operating conditions of the mesophilic system for WAS and FW codigestion using low-magnitude loading increments.
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Affiliation(s)
- Bao-Shan Xing
- State International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, MOE Key Lab of Northwest Water Resource, Environment and Ecology, Shaanxi Provincial Engineering Technology Research Center for Wastewater Treatment and Reuse, Shaanxi Provincial Key Lab of Environmental Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an, 710055, China.
| | - Xi-Fang Tang
- State International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, MOE Key Lab of Northwest Water Resource, Environment and Ecology, Shaanxi Provincial Engineering Technology Research Center for Wastewater Treatment and Reuse, Shaanxi Provincial Key Lab of Environmental Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an, 710055, China
| | - Ru Wang
- State International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, MOE Key Lab of Northwest Water Resource, Environment and Ecology, Shaanxi Provincial Engineering Technology Research Center for Wastewater Treatment and Reuse, Shaanxi Provincial Key Lab of Environmental Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an, 710055, China
| | - Sifan Cao
- State International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, MOE Key Lab of Northwest Water Resource, Environment and Ecology, Shaanxi Provincial Engineering Technology Research Center for Wastewater Treatment and Reuse, Shaanxi Provincial Key Lab of Environmental Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an, 710055, China
| | - Junwei Wen
- State International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, MOE Key Lab of Northwest Water Resource, Environment and Ecology, Shaanxi Provincial Engineering Technology Research Center for Wastewater Treatment and Reuse, Shaanxi Provincial Key Lab of Environmental Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an, 710055, China
| | - Yi Zhang
- State International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, MOE Key Lab of Northwest Water Resource, Environment and Ecology, Shaanxi Provincial Engineering Technology Research Center for Wastewater Treatment and Reuse, Shaanxi Provincial Key Lab of Environmental Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an, 710055, China
| | - Xiang-Lin Chang
- State International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, MOE Key Lab of Northwest Water Resource, Environment and Ecology, Shaanxi Provincial Engineering Technology Research Center for Wastewater Treatment and Reuse, Shaanxi Provincial Key Lab of Environmental Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an, 710055, China
| | - Xiaochang C Wang
- State International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, MOE Key Lab of Northwest Water Resource, Environment and Ecology, Shaanxi Provincial Engineering Technology Research Center for Wastewater Treatment and Reuse, Shaanxi Provincial Key Lab of Environmental Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an, 710055, China
| | - Rong Chen
- State International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, MOE Key Lab of Northwest Water Resource, Environment and Ecology, Shaanxi Provincial Engineering Technology Research Center for Wastewater Treatment and Reuse, Shaanxi Provincial Key Lab of Environmental Engineering, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an, 710055, China.
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Wen P, Wang Y, Huang W, Wang W, Chen T, Yu Z. Linking Microbial Community Succession With Substance Transformation in a Thermophilic Ectopic Fermentation System. Front Microbiol 2022; 13:886161. [PMID: 35602041 PMCID: PMC9116721 DOI: 10.3389/fmicb.2022.886161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/23/2022] [Indexed: 12/02/2022] Open
Abstract
Ectopic fermentation system (EFS) is an effective technology for treating mass livestock manure. However, the associations between microbial communities and substance transformation remain controversial. This study aimed to investigate chicken manure EFS lasting 170 days using 16S rRNA sequencing and electrochemical, spectroscopic, and chromatographic analyses. The results showed a noticeable transformation of protein-like substances into humus-like substances. Meanwhile, the electron–accepting capacity increased persistently, effectively reflecting the humification of organic substances. The contents of phenols that promoted electron transfer continued to increase from 2.80 to 6.00%, which could be used as a maturity indicator for EFS. During the heating period, the dominant microbial communities were Chloroflexi and Proteobacteria, whereas thermotolerant bacteria Cyanobacteria and Planctomycetes were significantly enriched from 1.64 to 50.15% during the continuous thermophilic period of EFS. The correlation analysis manifested that these thermotolerant bacteria were the major functional bacteria for the formation of phenols and the key to driving the humification of organic substances. This study provides insights into understanding the humification mechanisms and implementing regulatory strategies in EFS.
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Affiliation(s)
- Ping Wen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China.,Environmental Research Institute, School of Environment, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China
| | - Yueqiang Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China
| | - Wenfeng Huang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China
| | - Weiwu Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China
| | - Tao Chen
- Environmental Research Institute, School of Environment, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China
| | - Zhen Yu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China
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Rivas-Párraga R, Izquierdo A, Sánchez K, Bolaños-Guerrón D, Alfaro-Núñez A. Identification and phylogenetic characterization based on DNA sequences from RNA ribosomal genes of thermophilic microorganisms in a high elevation Andean tropical geothermal spring. BIONATURA 2022. [DOI: 10.21931/rb/2022.07.02.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Several microorganisms can survive in harsh acid environments in geothermal springs at high temperatures across the Equatorial Andes Mountains. However, little is known about their physiological features and phylogenetic composition. Here we identify thermophilic microorganisms (bacteria, fungi, and microalgae) hosted in an almost unexplored geothermal spring (known as “Aguas Hediondas”). The phylogeny of the cultures was determined by analyzing physiological features and DNA sequences of PCR products for 16S rRNA, ITS, and 23S rRNA genes. Twenty pure cultures were isolated from the samples, including 17 for bacteria, one for cyanobacterium, one for eukaryotic microalgae, and one for fungus. Most bacterial strains were gram-positive, spore-forming, and bacilli (Bacillus). Cyanobacterium strain belonged to Chroococcidiopsis and the eukaryotic microalgae to Chlorophyta. The unique fungal strain isolated was closely related to T. duponti. Through our study, isolated thermophilic bacteria, microalgae and fungi from the “Aguas Hediondas” geothermal spring were characterized and identified. This study represents one of the first extensive molecular characterizations of extremophile microbes in the Tropical Equatorial Andes.
Keywords. microbial diversity; DNA markers; extremophiles; phylogenetics
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Affiliation(s)
- Roque Rivas-Párraga
- Life science and Agriculture Department. Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador
| | - Andrés Izquierdo
- Life science and Agriculture Department. Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador Centro de Nanociencia y Nanotecnología (CENCINAT), Universidad de las Fuerzas Armadas ESPE, Av. Gral. Rumiñahui s/n, P.O. Box 171-5-231B, Sangolquí, Ecuador Ecuador Grupo de Investigación en Microbiología y Ambiente (GIMA), Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador
| | - Karen Sánchez
- School of Biological Sciences and Engineering, Yachay Tech University, San Miguel de Urcuqui, Ecuador
| | - Darío Bolaños-Guerrón
- Department of Earth Science and Constructions, Geographical and Environmental Engineering, Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador Centro de Nanociencia y Nanotecnología (CENCINAT), Universidad de las Fuerzas Armadas ESPE, Av. Gral. Rumiñahui s/n, P.O. Box 171-5-231B, Sangolquí, Ecuador Ecuador
| | - Alonzo Alfaro-Núñez
- Clinical Biochemistry Department, Næstved Hospital, Ringstegade 57a, 4700 Næstved, Denmark 5 Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353 Copenhagen K, Denmark
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Wen P, Tang J, Wang Y, Liu X, Yu Z, Zhou S. Hyperthermophilic composting significantly decreases methane emissions: Insights into the microbial mechanism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 784:147179. [PMID: 33894609 DOI: 10.1016/j.scitotenv.2021.147179] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/28/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Methane (CH4) emissions from thermophilic composting (TC) are a substantial contributor to climate change. Hyperthermophilic composting (HTC) can influence CH4-related microbial communities at temperatures up to 80 °C, and thus impact the CH4 emissions during composting. This work investigated CH4 emissions in sludge-derived HTC, and explored microbial community succession with quantitative PCR and high-throughput sequencing. Results demonstrated that HTC decreased CH4 emissions by 52.5% compared with TC. In HTC, the CH4 production potential and CH4 oxidation potential were nearly 40% and 64.1% lower than that of TC, respectively. There was a reduction in the quantity of mcrA (3.7 × 108 to 0 g-1 TS) in HTC, which was more significant than the reduction in pmoA (2.0 × 105 to 2.1 × 104 g-1 TS), and thus lead to reduce CH4 emissions. It was found that the abundance of most methanogens and methanotrophs was inhibited in the hyperthermal environment, with a decline in Methanosarcina, Methanosaeta and Methanobrevibacter potentially being responsible for reducing the CH4 emissions in HTC. This work provides important insight into mitigating CH4 emissions in composting.
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Affiliation(s)
- Ping Wen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Jia Tang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Yueqiang Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Xiaoming Liu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Zhen Yu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
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Gut bacterial profile in Indian children of varying nutritional status: a comparative pilot study. Eur J Nutr 2021; 60:3971-3985. [PMID: 33929588 PMCID: PMC8085102 DOI: 10.1007/s00394-021-02571-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/19/2021] [Indexed: 12/15/2022]
Abstract
PURPOSE Childhood malnutrition is a multifactorial disease, responsible for nearly half of all deaths in children under five. Lately, the probable association of a dysbiotic gut to malnutrition is also being eagerly investigated. The current study is an attempt to investigate this purported association through assessing the abundance of major gut bacterial phyla (Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria), probionts (Bifidobacteria and Lactobacillus), butyrogens (Faecalibacterium and Roseburia) and pathogens (Escherichia and Klebsiella). METHODS The study was conducted in the suburbs of Chandigarh, India in the year 2017. The children enrolled in the study were part of Anganwadis (Rural Child Care Centres) set up under Integrated Child Development Scheme (ICDS) of Government of India where community-based management approach is being widely used for treatment of malnutrition. We used qPCR based absolute quantification as well as the 16S rRNA amplicon sequencing approach for our study. The study population included 30 children in the age group of 2-5 years who were categorized into three groups Healthy, Moderate Acute Malnutrition (MAM) and Severe Acute Malnutrition (SAM), with 10 children in each group. The selection of participants was made based on Z scores. Further, statistical tools like the One-way ANOVA, PCA and PLSDA were employed to analyze and compare the gut bacterial profile. RESULTS Our investigation through the qPCR (Absolute quantification) approach revealed a significantly higher abundance of Actinobacteria in healthy, in comparison to children suffering from Severe Acute Malnutrition (SAM). Consequently, the same trend was also reflected with respect to Bifidobacterium, a prominent member of the Actinobacteria phylum. Conversely, a significant higher abundance of Lactobacillus with the diminishing nutritional status was recorded. Escherichia showed a significant higher abundance in healthy subjects compared to the malnourished; however, no such difference in abundance of Klebsiella was observed. The other target phyla [Bacteroidetes, Firmicutes and Proteobacteria] and genera (Faecalibacterium and Roseburia) showed differences in abundance; however, these were non-significant. Similarly, the bacterial taxonomy analysis of 16S rRNA gene amplicon sequencing data revealed the higher abundance of phylum Actinobacteria and its member Bifidobacterium with lower prevalence of Lactobacillus in healthy children. CONCLUSION The pattern of gut microbiota profile in malnourished subjects suggests a dysbiotic gut depleted in Bifidobacteria, a core member of the consortia of beneficial anaerobes of the healthy child gut.
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Bezdekova J, Vodova M, Dolezelikova K, Zitka J, Smerkova K, Zitka O, Adam V, Vaculovicova M. Detection of microbial contamination based on uracil-selective synthetic receptors. Talanta 2021; 224:121813. [PMID: 33379038 DOI: 10.1016/j.talanta.2020.121813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/22/2022]
Abstract
The here presented work is focused on the development of a method for detection of microbial contamination of food based on uracil-selective synthetic receptors. Because uracil may serve as an indicator of bacterial contamination, its selective and on-site detection may prevent spreading of foodborne diseases. The synthetic receptors were created by molecular imprinting. Molecularly imprinted polymers for selective uracil isolation were prepared by a non-covalent imprinting method using dopamine as a functional monomer. Detection of isolated uracil was performed by capillary electrophoresis with absorption detection (λ - 260 nm). The conditions of preparation of molecularly imprinted polymers, their binding properties, adsorption kinetics and selectivity were investigated in detail. Furthermore, the prepared polymer materials were used for selective isolation and detection of uracil from complex samples as tomato products by miniaturized electrophoretic system suggesting the potential of in situ analysis of real samples.
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Affiliation(s)
- Jaroslava Bezdekova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic
| | - Milada Vodova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic
| | - Kristyna Dolezelikova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic
| | - Jan Zitka
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic
| | - Kristyna Smerkova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic
| | - Ondrej Zitka
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic
| | - Marketa Vaculovicova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic.
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10
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Ramos‐Romero S, Léniz A, Martínez‐Maqueda D, Amézqueta S, Fernández‐Quintela A, Hereu M, Torres JL, Portillo MP, Pérez‐Jiménez J. Inter‐Individual Variability in Insulin Response after Grape Pomace Supplementation in Subjects at High Cardiometabolic Risk: Role of Microbiota and miRNA. Mol Nutr Food Res 2020; 65:e2000113. [DOI: 10.1002/mnfr.202000113] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 10/30/2020] [Indexed: 12/29/2022]
Affiliation(s)
- Sara Ramos‐Romero
- Institute of Advanced Chemistry of Catalonia (IQAC‐CSIC) Barcelona 08034 Spain
- Department of Cell Biology Physiology and Immunology Faculty of Biology University of Barcelona Barcelona 08028 Spain
| | - Asier Léniz
- Basque Health Service (Osakidetza) Araba Integrated Health Care Organization Vitoria 01009 Spain
- Nutrition and Obesity Group, Department of Nutrition and Food Science Faculty of Pharmacy and Lucio Lascaray Research Center University of the Basque Country (UPV/EHU) Vitoria 01006 Spain
| | - Daniel Martínez‐Maqueda
- Department of Metabolism and Nutrition Technology and Nutrition (ICTAN‐CSIC) Institute of Food Science José Antonio Novais 10 Madrid 28040 Spain
| | - Susana Amézqueta
- Departament d'Enginyeria Química i Química Analítica and Institut de Biomedicina (IBUB) Universitat de Barcelona Barcelona 08028 Spain
| | - Alfredo Fernández‐Quintela
- Nutrition and Obesity Group, Department of Nutrition and Food Science Faculty of Pharmacy and Lucio Lascaray Research Center University of the Basque Country (UPV/EHU) Vitoria 01006 Spain
- Instituto de Salud Carlos III (ISCIII) CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN) Madrid 28029 Spain
| | - Mercè Hereu
- Institute of Advanced Chemistry of Catalonia (IQAC‐CSIC) Barcelona 08034 Spain
| | - Josep Luís Torres
- Institute of Advanced Chemistry of Catalonia (IQAC‐CSIC) Barcelona 08034 Spain
| | - María P. Portillo
- Nutrition and Obesity Group, Department of Nutrition and Food Science Faculty of Pharmacy and Lucio Lascaray Research Center University of the Basque Country (UPV/EHU) Vitoria 01006 Spain
- Instituto de Salud Carlos III (ISCIII) CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN) Madrid 28029 Spain
| | - Jara Pérez‐Jiménez
- Department of Metabolism and Nutrition Technology and Nutrition (ICTAN‐CSIC) Institute of Food Science José Antonio Novais 10 Madrid 28040 Spain
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11
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Rodríguez-Saavedra M, González de Llano D, Moreno-Arribas MV. Beer spoilage lactic acid bacteria from craft brewery microbiota: Microbiological quality and food safety. Food Res Int 2020; 138:109762. [PMID: 33292943 DOI: 10.1016/j.foodres.2020.109762] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 09/27/2020] [Accepted: 09/28/2020] [Indexed: 01/28/2023]
Abstract
Craft beer is more susceptible to microbial spoilage because it does not have a pasteurization or filtration process, with lactic acid bacteria (LAB) being the most common beer spoilage microorganism. The aim of this study was to isolate LAB in a craft brewery and their characterization from a food safety and microbiological quality perspective, with a special focus on their abilities to produce biogenic amines (BA) and spoil the beer. The results of 60 monitored points inside the craft brewery showed that LAB associated with the craft brewing processes belonged to Lactobacillus, Pediococcus, and Leuconostoc genera, and most of them were detected in the filling area, which can lead to secondary contamination. Two isolates of L. brevis showed the most significant beer spoilage ability because they could grow in more acidic conditions, at a higher hop and alcohol content, and they displayed horA, horC, and hitA genes, which spoiled the vast majority of the tested beers. In addition, the aforementioned L. brevis isolates showed the highest BA production.
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Affiliation(s)
- Magaly Rodríguez-Saavedra
- Instituto de Investigación en Ciencias de la Alimentación (CIAL), CSIC-UAM, c/Nicolás Cabrera, 9. Campus de Cantoblanco, 28049 Madrid, Spain
| | - Dolores González de Llano
- Instituto de Investigación en Ciencias de la Alimentación (CIAL), CSIC-UAM, c/Nicolás Cabrera, 9. Campus de Cantoblanco, 28049 Madrid, Spain
| | - M Victoria Moreno-Arribas
- Instituto de Investigación en Ciencias de la Alimentación (CIAL), CSIC-UAM, c/Nicolás Cabrera, 9. Campus de Cantoblanco, 28049 Madrid, Spain.
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12
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Im S, Mostafa A, Shin SR, Kim DH. Combination of H 2SO 4-acidification and temperature-decrease for eco-friendly storage of pig slurry. JOURNAL OF HAZARDOUS MATERIALS 2020; 399:123063. [PMID: 32512282 DOI: 10.1016/j.jhazmat.2020.123063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/09/2020] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
Owing to the economic benefit and efficiency, H2SO4-acidification is often applied for reducing CH4 emissions during storage of pig slurry (PS). However, it encounters with several problems related with safety and the concomitant H2S emissions. To reduce the required amount of H2SO4, in this study, the storage at low temperature (20-35 °C) was applied to the mild-acidified PS (pH 6.5 and 7.0). 55.1 kg CO2 eq./ton PS of CH4 was emitted from the control (non-acidified at 35 °C), which was reduced to 14.4-40.2 kg CO2 eq./ton PS at 20-30 °C. Temperature-decrease led to the increase of the abundance of methanogens (Methanobrevibacter and Methanolobus) that can grow at low temperature and the drop of specific methanogenic activity value. To achieve 70 % CH4 reduction, 1.6 kg H2SO4/ton PS was needed in PS acidification, which was decreased to 0.5 kg H2SO4/ton PS by decreasing temperature from 35 °C to 25 °C. CH4 production potential of the PS stored at 35 °C-pH 6.5 and 25 °C-pH 7.0 was increased by 21-33 % compared to the control. The GHG reduction of 33.6-41.9 kg CO2 eq./ton PS and the profit of 6.6 USD/ton PS could be attained by applying acidification or combined storage, indicating that the temperature-decrease can be effectively combined with H2SO4-acidification.
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Affiliation(s)
- Seongwon Im
- Department of Civil Engineering, Inha University, 100 Inharo, Nam-gu, Incheon 22212, Republic of Korea
| | - Alsayed Mostafa
- Department of Civil Engineering, Inha University, 100 Inharo, Nam-gu, Incheon 22212, Republic of Korea
| | - Sang-Ryong Shin
- Process design team, JEON TECH. Co., Ltd., 77 Haenggung-ro, Paldal-gu, Suwon 16261, Republic of Korea
| | - Dong-Hoon Kim
- Department of Civil Engineering, Inha University, 100 Inharo, Nam-gu, Incheon 22212, Republic of Korea.
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13
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Cao X, Tang L, Zeng Z, Wang B, Zhou Y, Wang Q, Zou P, Li W. Effects of Probiotics BaSC06 on Intestinal Digestion and Absorption, Antioxidant Capacity, Microbiota Composition, and Macrophage Polarization in Pigs for Fattening. Front Vet Sci 2020; 7:570593. [PMID: 33240950 PMCID: PMC7677304 DOI: 10.3389/fvets.2020.570593] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/29/2020] [Indexed: 01/24/2023] Open
Abstract
This study aimed to compare the effects of BaSC06 and antibiotics on growth, digestive functions, antioxidant capacity, macrophage polarization, and intestinal microbiota of pigs for fattening. A total of 117 pigs for fattening with similar weight and genetic basis were divided into 3 groups: Anti group (containing 40 g/t Kitasamycin in the diet), Anti+Ba group (containing 20 g/t Kitasamycin and 0.5 × 108 CFU/kg BaSC06 in the diet) and Ba group (containing 1 × 108 cfu/Kg BaSC06 in the diet without any antibiotics). Each treatment was performed in three replicates with 13 pigs per replicate. Results showed that BaSC06 replacement significantly improved the ADG (P < 0.05), intestinal digestion and absorption function by increasing the activity of intestinal digestive enzymes and the expression of glucose transporters SGLT1 (P < 0.05) and small peptide transporters PEPT1 (P < 0.05). Besides, BaSC06 supplementation enhanced intestinal and body antioxidant capacity by activating the Nrf2/Keap1 antioxidant signaling pathway due to the increased expression of p-Nrf2 (P < 0.05). Notably, BaSC06 alleviated intestinal inflammation by inhibiting the production of pro-inflammatory cytokines, IL-8, IL-6, and MCP1 (P < 0.05), and simultaneously increasing the expression of M1 macrophage marker protein iNOS (P < 0.05) and M2 macrophage marker protein Arg (P < 0.05) in the intestinal mucosa. Moreover, BaSC06 promoted the polarization of macrophages to M2 phenotype by stimulating the STAT3 signaling pathway. It was also noted that BaSC06 improved microbiota composition by enhancing the proportion of Firmicutes, and reducing that of Bacteroidetes and Proteobacteria. Taken together, our results indicate that dietary supplementation of BaSC06 in pigs for fattening improves the growth, mucosal structure, antioxidative capacity, immune functions (including increasing M1 and M2 polarization of macrophage) and composition of intestinal microbiota, which is much better than antibiotics, suggesting that it is an effective alternative to antibiotics in the preparation of pig feed.
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Affiliation(s)
| | | | | | | | | | | | | | - Weifen Li
- Key Laboratory of Molecular Animal Nutrition of the Ministry of Education, Institute of Feed Science, College of Animal Sciences, Zhejiang University, and Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, China
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14
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Rodríguez-Saavedra M, González de Llano D, Beltran G, Torija MJ, Moreno-Arribas MV. Pectinatus spp. - Unpleasant and recurrent brewing spoilage bacteria. Int J Food Microbiol 2020; 336:108900. [PMID: 33129006 DOI: 10.1016/j.ijfoodmicro.2020.108900] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 09/19/2020] [Accepted: 10/02/2020] [Indexed: 12/20/2022]
Abstract
Traditionally, beer has been recognised as a beverage with high microbiological stability because of the hostile growth environment posed by beer and increasing attention being paid to brewery hygiene. However, the microbiological risk has increased in recent years because of technological advances toward reducing oxygen in beers, besides the increase in novel beer styles production, such as non-pasteurised, flash pasteurised, cold sterilised, mid-strength, and alcoholic-free beer, that are more prone to spoilage bacteria. Moreover, using innovative beer ingredients like fruits and vegetables is an added cause of microbial spoilage. To maintain quality and good brand image, beer spoilage microorganisms are a critical concern for breweries worldwide. Pectinatus and Megasphaera are Gram-negative bacteria mostly found in improper brewing environments, leading to consumer complaints and financial losses. Because of the lack of compiled scientific knowledge on Pectinatus spoilage ability, this review provides a comprehensive overview of the occurrence, survival mechanisms, and the factors affecting beer spoilage Pectinatus species in the brewing process.
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Affiliation(s)
- Magaly Rodríguez-Saavedra
- Instituto de Investigación en Ciencias de la Alimentación (CIAL), CSIC-UAM, c/ Nicolás Cabrera, 29049 Madrid, Spain
| | - Dolores González de Llano
- Instituto de Investigación en Ciencias de la Alimentación (CIAL), CSIC-UAM, c/ Nicolás Cabrera, 29049 Madrid, Spain
| | - Gemma Beltran
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Marcel·lí Domingo, 1, 43007 Tarragona, Spain
| | - María-Jesús Torija
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Marcel·lí Domingo, 1, 43007 Tarragona, Spain
| | - M Victoria Moreno-Arribas
- Instituto de Investigación en Ciencias de la Alimentación (CIAL), CSIC-UAM, c/ Nicolás Cabrera, 29049 Madrid, Spain.
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15
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Dash HR, Das S. Thanatomicrobiome and epinecrotic community signatures for estimation of post-mortem time interval in human cadaver. Appl Microbiol Biotechnol 2020; 104:9497-9512. [PMID: 33001249 DOI: 10.1007/s00253-020-10922-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/15/2020] [Accepted: 09/21/2020] [Indexed: 12/12/2022]
Abstract
Estimation of post-mortem time interval (PMI) is a key parameter in the forensic investigation which poses a huge challenge to the medico-legal experts. The succession of microbes within different parts of the human body after death has shown huge potential in the determination of PMI. Human body harbors trillions of microorganisms as commensals. With the death of an individual when biological functions are stopped, these microorganisms behave contrarily along with the invasion of degrading microbes from the environment. Human cadaver becomes a rich source of nutrients due to autolysis of cells, which attracts various invading microorganisms as well as macroorganisms. At different stages of degradation, the succession of microorganisms differs significantly which can be explored for accurate PMI estimation. With the advent of microbial genomics technique and reduction in the cost of DNA sequencing, thanatomicrobiome and epinecrotic community analysis have gained huge attention in PMI estimation. The article summarizes different sources of microorganisms in a human cadaver, their succession pattern, and analytical techniques for application in the field of microbial forensics. KEY POINTS: • Thanatomicrobiome and epinecrotic microbiome develop in postmortem human body. • Lack of metabolic, immune, neuroendocrine systems facilitate microbial succession. • Analysis of postmortem microbial communities predicts accurate PMI.
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Affiliation(s)
- Hirak Ranjan Dash
- Forensic Science Laboratory, Bhadbhada Road, Bhopal, Madhya Pradesh, 462003, India.
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India.
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16
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Ramos-Romero S, Martínez-Maqueda D, Hereu M, Amézqueta S, Torres JL, Pérez-Jiménez J. Modifications of Gut Microbiota after Grape Pomace Supplementation in Subjects at Cardiometabolic Risk: A Randomized Cross-Over Controlled Clinical Trial. Foods 2020; 9:foods9091279. [PMID: 32933009 PMCID: PMC7555163 DOI: 10.3390/foods9091279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/01/2020] [Accepted: 09/07/2020] [Indexed: 02/08/2023] Open
Abstract
Polyphenols are dietary bioactive compounds able to induce modifications in the gut microbiota profile, although more clinical studies are needed. With this aim, a randomized cross-over clinical trial was conducted, where 49 subjects at cardiometabolic risk (exhibiting at least two metabolic syndrome factors) were supplemented with a daily dose of 8 g of grape pomace (GP) for 6 weeks, with an equivalent control (CTL) period. The levels of total bacteria and Bacteroidetes, Firmicutes, Lactobacilliales, Bacteroides and Prevotella were estimated in fecal DNA by quantitative real-time PCR (qPCR), while fecal short-chain fatty acids (SCFAs) were assessed by gas chromatography. Several cardiometabolic markers were evaluated in blood samples. GP reduced insulin levels only in half of the participants (responders). GP supplementation did not cause significant modifications in the microbiota profile of the whole group, except for a tendency (p = 0.059) towards a decrease in the proportion of Lactobacilliales, while it increased the proportion of Bacteroides in non-responder subjects. The reduction of insulin levels in subjects at cardiometabolic risk upon GP supplementation appears not to be induced by changes in the major subgroups of gut microbiota. Further studies at the species level may help to elucidate the possible role of microbiota in GP-induced insulinemic status.
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Affiliation(s)
- Sara Ramos-Romero
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; (S.R.-R.); (M.H.); (J.L.T.)
- Department of Cell Biology, Physiology & Immunology, Faculty of Biology, University of Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain
| | - Daniel Martínez-Maqueda
- Department of Metabolism and Nutrition, Institute of Food Science, Technology and Nutrition (ICTAN-CSIC), José Antonio Novais 10, 28040 Madrid, Spain;
| | - Mercè Hereu
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; (S.R.-R.); (M.H.); (J.L.T.)
| | - Susana Amézqueta
- Departament d’Enginyeria Química i Química Analítica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Carrer de Martí i Franquès, 1-11, 08028 Barcelona, Spain;
| | - Josep Lluís Torres
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; (S.R.-R.); (M.H.); (J.L.T.)
| | - Jara Pérez-Jiménez
- Department of Metabolism and Nutrition, Institute of Food Science, Technology and Nutrition (ICTAN-CSIC), José Antonio Novais 10, 28040 Madrid, Spain;
- Correspondence: ; Tel.: +34-915-492-300
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17
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Suzuki K. Emergence of New Spoilage Microorganisms in the Brewing Industry and Development of Microbiological Quality Control Methods to Cope with This Phenomenon: A Review. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2020. [DOI: 10.1080/03610470.2020.1782101] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Koji Suzuki
- Asahi Quality and Innovations, Ltd, Moriya, Ibaraki, Japan
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18
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In Situ Profiling of the Three Dominant Phyla Within the Human Gut Using TaqMan PCR for Pre-Hospital Diagnosis of Gut Dysbiosis. Int J Mol Sci 2020; 21:ijms21061916. [PMID: 32168885 PMCID: PMC7139488 DOI: 10.3390/ijms21061916] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/05/2020] [Accepted: 03/09/2020] [Indexed: 12/26/2022] Open
Abstract
A microbial imbalance called dysbiosis leads to inflammatory bowel disease (IBD), which can include ulcerative colitis (UC). Fecal microbiota transplantation (FMT), a novel therapy, has recently been successful in treating gut dysbiosis in UC patients. For the FMT technique to be successful, the gut microbiota of both the healthy donors and UC patients must be characterized. For decades, next-generation sequencing (NGS) has been used to analyze gut microbiota. Despite the popularity of NGS, the cost and time constraints make it difficult to use in emergency services and activities related to the periodic monitoring of microbiota profile alterations. Hence, in this study, we developed a multiplex TaqMan qPCR assay (MTq-PCR) with novel probes to simultaneously determine the relative proportions of the three dominant microbial phyla in the human gut: Bacteroidetes, Firmicutes, and Proteobacteria. The relative proportions of the three phyla in fecal samples of either healthy volunteers or UC patients were similar when assessed NGS and the MTq-PCR. Thus, our MTq-PCR assay could be a practical microbiota profiling alternative for diagnosing and monitoring gut dysbiosis in UC patients during emergency situations, and it could have a role in screening stool from potential FMT donors.
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Demirci M, Bahar Tokman H, Taner Z, Keskin FE, Çağatay P, Ozturk Bakar Y, Özyazar M, Kiraz N, Kocazeybek BS. Bacteroidetes and Firmicutes levels in gut microbiota and effects of hosts TLR2/TLR4 gene expression levels in adult type 1 diabetes patients in Istanbul, Turkey. J Diabetes Complications 2020; 34:107449. [PMID: 31677982 DOI: 10.1016/j.jdiacomp.2019.107449] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 09/03/2019] [Accepted: 09/08/2019] [Indexed: 02/08/2023]
Abstract
AIM The aim of this study was to determine and compare the levels of both Bacteroidetes and Firmicutes in the gut microbiota and TLR2/TLR4 gene expression in the blood of patients with type 1 diabetes mellitus (T1DM) and healthy individuals. These results may serve as a preliminary assessment to guide future research. METHOD Between January and October 2014, stool and blood samples were collected from 53 adult T1DM patients and 53 age- and gender-matched healthy individuals. Bacteroidetes and Firmicutes levels were assessed from stool sample DNA and TLR2 and TLR4 expression levels were analyzed via qPCR using RNA from EDTA blood samples from both patients and healthy controls. RESULTS The amounts of Bacteroidetes and Firmicutes were statistically significantly higher and lower, respectively, in the T1DM group than in the healthy control group (p < 0.001 and p < 0.001, respectively). In addition, the Firmicutes/Bacteroidetes ratios in patients with T1DM were significantly lower than in healthy controls. The TLR4 and TLR2 gene expression levels in T1DM patients were significantly upregulated and downregulated, respectively, compared to those in the control group. CONCLUSION Our data are the first to show a relationship between T1DM and gut microbiota in our country. In addition, our results provide information about the connections between T1DM, gut microbiota, and TLR2 and TLR4 expression. We believe that Bacteroidetes and Firmicutes in the gut microbiota may play a role in the autoimmune process of T1DM and that these findings should be further investigated in the future.
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Affiliation(s)
- Mehmet Demirci
- Department of Medical Microbiology, Beykent University, School of Medicine, Istanbul, Turkey
| | - Hrisi Bahar Tokman
- Department of Medical Microbiology, Cerrahpasa School of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey.
| | - Zeynep Taner
- Department of Medical Microbiology, Cerrahpasa School of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Fatma Ela Keskin
- Department of Endocrinology, Gaziosmanpasa Taksim Training and Research Hospital, Health Sciences University, Istanbul, Turkey
| | - Penbe Çağatay
- Vocational School of Health Service, Department of Medical Services and Technics, Istanbul University - Cerrahpasa, Istanbul, Turkey
| | - Yesim Ozturk Bakar
- Department of Medical Microbiology, Cerrahpasa School of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Mücahit Özyazar
- Department of Endocrinology, Gaziosmanpasa Hospital, Yeni Yuzyil University, Medical Faculty, Istanbul, Turkey
| | - Nuri Kiraz
- Department of Medical Microbiology, School of Medicine, Namık Kemal University, Tekirdağ, Turkey
| | - Bekir S Kocazeybek
- Department of Medical Microbiology, Cerrahpasa School of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
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20
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Li X, Shi XS, Lu MY, Zhao YZ, Li X, Peng H, Guo RB. Succession of the bacterial community and functional characteristics during continuous thermophilic composting of dairy manure amended with recycled ceramsite. BIORESOURCE TECHNOLOGY 2019; 294:122044. [PMID: 31520859 DOI: 10.1016/j.biortech.2019.122044] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 06/10/2023]
Abstract
This study aimed to investigate variations of bacterial community and functional characteristics during the continuous thermophilic composting (CTC). Also their differences were discussed when amended with ceramsite and recycled ceramsite as the porous bulking agent. Results showed that the bacterial community shifted greatly and bacterial diversity increased as the CTC proceeded. Firmicutes and Chloroflexi was one of the major phyla at the active and late phase respectively. While Actinobacteria was the dominant phyla during the whole CTC. With the addition of ceramsite and recycled ceramsite, no significant difference was found of the overall bacterial variation trends. But the major phyla of Chloroflexi and Actinobacteria and major genes related to amino acid metabolism and carbohydrate metabolism increased significantly, especially when the recycled ceramsite was added. Redundancy analysis indicated that the succession of bacterial community was tightly related with the pH, water soluble organic carbon, NH4+-N, organic matter and germination index.
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Affiliation(s)
- Xu Li
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xiao-Shuang Shi
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China
| | - Ming-Yi Lu
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yu-Zhong Zhao
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China
| | - Xiangqian Li
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian 223003, PR China
| | - Hui Peng
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Rong-Bo Guo
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China; Dalian National Laboratory for Clean Energy, Dalian 116023, PR China.
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21
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Hereu M, Ramos-Romero S, Marín-Valls R, Amézqueta S, Miralles-Pérez B, Romeu M, Méndez L, Medina I, Torres JL. Combined Buckwheat d-Fagomine and Fish Omega-3 PUFAs Stabilize the Populations of Gut Prevotella and Bacteroides While Reducing Weight Gain in Rats. Nutrients 2019; 11:nu11112606. [PMID: 31683529 PMCID: PMC6893428 DOI: 10.3390/nu11112606] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/23/2019] [Accepted: 10/28/2019] [Indexed: 12/18/2022] Open
Abstract
Some functional food components may help maintain homeostasis by promoting balanced gut microbiota. Here, we explore the possible complementary effects of d-fagomine and ω-3 polyunsaturated fatty acids (ω-3 PUFAs) eicosapentaenoic acid/docosahexaenoic acid (EPA/DHA 1:1) on putatively beneficial gut bacterial strains. Male Sprague–Dawley rats were supplemented with d-fagomine, ω-3 PUFAs, or both, for 23 weeks. Bacterial subgroups were evaluated in fecal DNA by quantitative real-time polymerase chain reaction (qRT-PCR) and short-chain fatty acids were determined by gas chromatography. We found that the populations of the genus Prevotella remained stable over time in animals supplemented with d-fagomine, independently of ω-3 PUFA supplementation. Animals in these groups gained less weight than controls and rats given only ω-3 PUFAs. d-Fagomine supplementation together with ω-3 PUFAs maintained the relative populations of Bacteroides. ω-3 PUFAs alone or combined with d-fagomine reduced the amount of acetic acid and total short-chain fatty acids in feces. The plasma levels of pro-inflammatory arachidonic acid derived metabolites, triglycerides and cholesterol were lower in both groups supplemented with ω-3 PUFAs. The d-fagomine and ω-3 PUFAs combination provided the functional benefits of each supplement. Notably, it helped stabilize populations of Prevotella in the rat intestinal tract while reducing weight gain and providing the anti-inflammatory and cardiovascular benefits of ω-3 PUFAs.
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Affiliation(s)
- Mercè Hereu
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), E-08034 Barcelona, Spain.
| | - Sara Ramos-Romero
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), E-08034 Barcelona, Spain.
- Department of Cell Biology, Physiology & Immunology, Faculty of Biology, University of Barcelona, E-08028 Barcelona, Spain.
| | - Roser Marín-Valls
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), E-08034 Barcelona, Spain.
| | - Susana Amézqueta
- Departament d'Enginyeria Química i Química Analítica and Institut de Biomedicina (IBUB), Universitat de Barcelona, E-08028 Barcelona, Spain.
| | - Bernat Miralles-Pérez
- Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, E-43201 Reus, Spain.
| | - Marta Romeu
- Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, E-43201 Reus, Spain.
| | - Lucía Méndez
- Instituto de Investigaciones Marinas (IIM-CSIC), E-36208 Vigo, Spain.
| | - Isabel Medina
- Instituto de Investigaciones Marinas (IIM-CSIC), E-36208 Vigo, Spain.
| | - Josep Lluís Torres
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), E-08034 Barcelona, Spain.
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Metataxonomics of Tunisian phosphogypsum based on five bioinformatics pipelines: Insights for bioremediation. Genomics 2019; 112:981-989. [PMID: 31220587 DOI: 10.1016/j.ygeno.2019.06.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 06/15/2019] [Indexed: 11/23/2022]
Abstract
Phosphogypsum (PG) is an acidic by-product from the phosphate fertilizer industry and it is characterized by a low nutrient availability and the presence of radionuclides and heavy metals which pose a serious problem in its management. Here, we have applied Illumina MiSeq sequencing technology and five bioinformatics pipelines to explore the phylogenetic communities in Tunisian PG. Taking One Codex as a reference method, we present the results of 16S-rDNA-gene-based metataxonomics abundances with four other alternative bioinformatics pipelines (MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST), mothur, MICrobial Community Analysis (MICCA) and Quantitative Insights into Microbial Ecology (QIIME)), when analyzing the Tunisian PG. Importantly, based on 16S rDNA datasets, the functional capabilities of microbial communities of PG were deciphered. They suggested the presence of PG autochthonous bacteria valorizable into (1) removal of radioactive elements and toxic heavy metals, (2) promotion of plant growth, (3) oxidation and (4) reduction of sulfate. These bacteria can be explored further for applications in the bioremediation of by-products, like PG, by different processes.
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Wang Y, Gong L, Wu YP, Cui ZW, Wang YQ, Huang Y, Zhang XP, Li WF. Oral administration of Lactobacillus rhamnosus GG to newborn piglets augments gut barrier function in pre-weaning piglets. J Zhejiang Univ Sci B 2019; 20:180-192. [PMID: 30666850 DOI: 10.1631/jzus.b1800022] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
To understand the effects of Lactobacillus rhamnosus GG (ATCC 53103) on intestinal barrier function in pre-weaning piglets under normal conditions, twenty-four newborn littermate piglets were randomly divided into two groups. Piglets in the control group were orally administered with 2 mL 0.1 g/mL sterilized skim milk while the treatment group was administered the same volume of sterilized skim milk with the addition of viable L. rhamnosus at the 1st, 3rd, and 5th days after birth. The feeding trial was conducted for 25 d. Results showed that piglets in the L. rhamnosus group exhibited increased weaning weight and average daily weight gain, whereas diarrhea incidence was decreased. The bacterial abundance and composition of cecal contents, especially Firmicutes, Bacteroidetes, and Fusobacteria, were altered by probiotic treatment. In addition, L. rhamnosus increased the jejunal permeability and promoted the immunologic barrier through regulating antimicrobial peptides, cytokines, and chemokines via Toll-like receptors. Our findings indicate that oral administration of L. rhamnosus GG to newborn piglets is beneficial for intestinal health of pre-weaning piglets by improving the biological, physical, and immunologic barriers of intestinal mucosa.
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Affiliation(s)
- Yang Wang
- Key Laboratory of Molecular Animal Nutrition and Feed Science, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Li Gong
- Key Laboratory of Molecular Animal Nutrition and Feed Science, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Yan-Ping Wu
- Key Laboratory of Molecular Animal Nutrition and Feed Science, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Zhi-Wen Cui
- Key Laboratory of Molecular Animal Nutrition and Feed Science, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Yong-Qiang Wang
- Department of Animal Sciences, Oregon State University, Corvallis, OR 97330, USA
| | - Yi Huang
- Key Laboratory of Molecular Animal Nutrition and Feed Science, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, College of Animal Science, Zhejiang University, Hangzhou 310058, China.,College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| | - Xiao-Ping Zhang
- China National Bamboo Research Center, Key Laboratory of High Efficient Processing of Bamboo of Zhejiang Province, Hangzhou 310012, China
| | - Wei-Fen Li
- Key Laboratory of Molecular Animal Nutrition and Feed Science, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, College of Animal Science, Zhejiang University, Hangzhou 310058, China
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Ramos-Romero S, Hereu M, Atienza L, Casas J, Jáuregui O, Amézqueta S, Dasilva G, Medina I, Nogués MR, Romeu M, Torres JL. Mechanistically different effects of fat and sugar on insulin resistance, hypertension, and gut microbiota in rats. Am J Physiol Endocrinol Metab 2018; 314:E552-E563. [PMID: 29351480 DOI: 10.1152/ajpendo.00323.2017] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Insulin resistance (IR) and impaired glucose tolerance (IGT) are the first manifestations of diet-induced metabolic alterations leading to Type 2 diabetes, while hypertension is the deadliest risk factor of cardiovascular disease. The roles of dietary fat and fructose in the development of IR, IGT, and hypertension are controversial. We tested the long-term effects of an excess of fat or sucrose (fructose/glucose) on healthy male Wistar-Kyoto (WKY) rats. Fat affects IR and IGT earlier than fructose through low-grade systemic inflammation evidenced by liver inflammatory infiltration, increased levels of plasma IL-6, PGE2, and reduced levels of protective short-chain fatty acids without triggering hypertension. Increased populations of gut Enterobacteriales and Escherichia coli may contribute to systemic inflammation through the generation of lipopolysaccharides. Unlike fat, fructose induces increased levels of diacylglycerols (lipid mediators of IR) in the liver, urine F2-isoprostanes (markers of systemic oxidative stress), and uric acid, and triggers hypertension. Elevated populations of Enterobacteriales and E. coli were only detected in rats given an excess of fructose at the end of the study. Dietary fat and fructose trigger IR and IGT in clearly differentiated ways in WKY rats: early low-grade inflammation and late direct lipid toxicity, respectively; gut microbiota plays a role mainly in fat-induced IR, and hypertension is independent of inflammation-mediated IR. The results provide evidence that suggests that the combination of fat and sugar is potentially more harmful than fat or sugar alone when taken in excess.
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Affiliation(s)
- Sara Ramos-Romero
- Institute of Advanced Chemistry of Catalonia, Consejo Superior de Investigaciones Científicas (IQAC-CSIC) , Barcelona , Spain
- Faculty of Biology, University of Barcelona , Barcelona , Spain
| | - Mercè Hereu
- Institute of Advanced Chemistry of Catalonia, Consejo Superior de Investigaciones Científicas (IQAC-CSIC) , Barcelona , Spain
| | - Lidia Atienza
- Department of Pathology, Puerta del Mar University Hospital , Cádiz , Spain
| | - Josefina Casas
- Research Unit on Bioactive Molecules, Department of Biomedicinal Chemistry, IQAC-CSIC, Barcelona , Spain
| | - Olga Jáuregui
- Scientific and Technological Centers of the University of Barcelona , Barcelona , Spain
| | - Susana Amézqueta
- Faculty of Chemistry, University of Barcelona , Barcelona , Spain
| | | | | | - Maria Rosa Nogués
- Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili, Reus, Spain
| | - Marta Romeu
- Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili, Reus, Spain
| | - Josep Lluís Torres
- Institute of Advanced Chemistry of Catalonia, Consejo Superior de Investigaciones Científicas (IQAC-CSIC) , Barcelona , Spain
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Pittet V, Haakensen M, Ziola B. Rapid Screening for Gram-Negative and Gram-Positive Beer-SpoilageFirmicutesUsing a Real-Time Multiplex PCR. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2010-0308-02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Vanessa Pittet
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Monique Haakensen
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Barry Ziola
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
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Bergsveinson J, Goerzen S, Redekop A, Zoerb S, Ziola B. Genetic Variability in the Hop-Tolerance horC Gene of Beer-Spoiling Lactic Acid Bacteria. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2016-3962-01] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Jordyn Bergsveinson
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Room 2841 Royal University Hospital, 103 Hospital Drive, Saskatoon, SK Canada S7N 0W8
| | - Scott Goerzen
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Room 2841 Royal University Hospital, 103 Hospital Drive, Saskatoon, SK Canada S7N 0W8
| | - Anna Redekop
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Room 2841 Royal University Hospital, 103 Hospital Drive, Saskatoon, SK Canada S7N 0W8
| | - Sheree Zoerb
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Room 2841 Royal University Hospital, 103 Hospital Drive, Saskatoon, SK Canada S7N 0W8
| | - Barry Ziola
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Room 2841 Royal University Hospital, 103 Hospital Drive, Saskatoon, SK Canada S7N 0W8
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Haakensen M, Pittet V, Morrow K, Schubert A, Ferguson J, Ziola B. Ability of Novel ATP-Binding Cassette Multidrug Resistance Genes to Predict Growth of Pediococcus Isolates in Beer. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2009-0601-01] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Monique Haakensen
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Vanessa Pittet
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kendra Morrow
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Alison Schubert
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Janet Ferguson
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Barry Ziola
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
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Lim JS, Yang SH, Kim BS, Lee EY. Comparison of microbial communities in swine manure at various temperatures and storage times. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 31:1373-1380. [PMID: 29381907 PMCID: PMC6043449 DOI: 10.5713/ajas.17.0704] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/21/2017] [Indexed: 11/27/2022]
Abstract
Objective This study was designed to investigate the effects of temperature and storage time on the evolution of bacterial communities in swine manure. Methods Manure was stored at −20°C, 4°C, 20°C, or 37°C and sampled at 7-day intervals over 28 days of storage, for a total of 5 time points. To assess the bacterial species present, 16S ribosomal RNA gene sequences were analyzed using pyrosequencing. Results After normalization, 113,934 sequence reads were obtained, with an average length of 466.6±4.4 bp. The diversity indices of the communities reduced as temperature and storage time increased, and the slopes of rarefaction curves decreased from the second week in samples stored at −20°C and 4°C. These results indicate that the richness of the bacterial community in the manure reduced as temperature and storage time increased. Firmicutes were the dominant phylum in all samples examined, ranging from 89.3% to 98.8% of total reads, followed by Actinobacteria, which accounted for 0.6% to 7.9%. A change in community composition was observed in samples stored at 37°C during the first 7 days, indicating that temperature plays an important role in determining the microbiota of swine manure. Clostridium, Turicibacter, Streptococcus, and Lactobacillus within Firmicutes, and Corynebacterium within Actinobacteria were the most dominant genera in fresh manure and all stored samples. Conclusion Based on our findings, we propose Clostridium as an indicator genus of swine manure decomposition in an anaerobic environment. The proportions of dominant genera changed in samples stored at 20°C and 37°C during the fourth week. Based on these results, it was concluded that the microbial communities of swine manure change rapidly as storage time and temperature increase.
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Affiliation(s)
- Joung-Soo Lim
- Animal Environment Division, National Institute of Animal Science, RDA, Wanju 55365, Korea
| | - Seung Hak Yang
- Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang, 25340, Korea
| | - Bong-Soo Kim
- Department of Life Science, Hallym University, Chuncheon 24252, Korea
| | - Eun Young Lee
- Department of Environmental and Energy Engineering, The University of Suwon, Suwon 18323, Korea
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Community and Proteomic Analysis of Anaerobic Consortia Converting Tetramethylammonium to Methane. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2017; 2017:2170535. [PMID: 29391857 PMCID: PMC5748143 DOI: 10.1155/2017/2170535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 09/25/2017] [Accepted: 10/31/2017] [Indexed: 11/17/2022]
Abstract
Tetramethylammonium-degrading methanogenic consortia from a complete-mixing suspended sludge (CMSS) and an upflow anaerobic sludge blanket (UASB) reactors were studied using multiple PCR-based molecular techniques and shotgun proteomic approach. The prokaryotic 16S rRNA genes of the consortia were analyzed by quantitative PCR, high-throughput sequencing, and DGGE-cloning methods. The results showed that methanogenic archaea were highly predominant in both reactors but differed markedly according to community structure. Community and proteomic analysis revealed that Methanomethylovorans and Methanosarcina were the major players for the demethylation of methylated substrates and methane formation through the reduction pathway of methyl-S-CoM and possibly, acetyl-CoA synthase/decarbonylase-related pathways. Unlike high dominance of one Methanomethylovorans population in the CMSS reactor, diverse methylotrophic Methanosarcina species inhabited in syntrophy-like association with hydrogenotrophic Methanobacterium in the granular sludge of UASB reactor. The overall findings indicated the reactor-dependent community structures of quaternary amines degradation and provided microbial insight for the improved understanding of engineering application.
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Ramos-Romero S, Hereu M, Molinar-Toribio E, Almajano MP, Méndez L, Medina I, Taltavull N, Romeu M, Nogués MR, Torres JL. Effects of the combination of ω-3 PUFAs and proanthocyanidins on the gut microbiota of healthy rats. Food Res Int 2017; 97:364-371. [PMID: 28578061 DOI: 10.1016/j.foodres.2017.04.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/06/2017] [Accepted: 04/23/2017] [Indexed: 11/26/2022]
Abstract
ω-3 Polyunsaturated fatty acids (PUFAs) reduce risk factors for cardiovascular diseases (CVD) and other pathologies that involve low-grade inflammation. They have recently been shown to exert complementary functional effects with proanthocyanidins. As the reduction of health-promoting gut bacteria such as lactobacilli and bifidobacteria has been linked to a number of alterations in the host, the aim of this study was to determine whether PUFAs and proanthocyanidins also cooperate in maintaining well-balanced microbiota. To this end, rats were supplemented for 6months with eicosapentaenoic acid (EPA)/docosahexaenoic acid (DHA) 1:1 (16.6g/kg feed); proanthocyanidin-rich grape seed extract (GSE, 0.8g/kg feed); or both. Plasma adiponectin, cholesterol, and urine nitrites were measured. Gut bacterial subgroups were evaluated in fecal DNA by qRT-PCR. Short-chain fatty acids (SCFAs) were determined in feces by gas chromatography. Body and adipose tissue weights were found to be higher in the animals given ω-3 PUFAs, while their energy intake was lower. Plasma cholesterol was lower in ω-3 PUFA supplemented groups, while adiponectin and urine nitrites were higher. ω-3 PUFAs reduced the population of Lactobacillales and L. acidophilus after 6months of supplementation. GSE significantly reduced L. plantarum and B. longum. The combination of ω-3 PUFAs and GSE maintained the health-promoting bacteria at levels similar to those of the control group. Acetic acid was increased by the ω-3 PUFA individual supplementation, while the combination with GSE kept this value similar to the control value. In conclusion, while individual supplementations with ω-3 PUFAs or GSE modify the populations of Lactobacillus, Bifidobacterium and microbial products (SCFAs), their combination maintains the standard proportions of these bacterial subgroups and their function while also providing the cardiovascular benefits of ω-3 PUFAs.
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Affiliation(s)
- Sara Ramos-Romero
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona, Spain.
| | - Mercè Hereu
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona, Spain.
| | | | - María Pilar Almajano
- Chemical Engineering Department, Technical University of Catalonia, Barcelona, Spain.
| | - Lucía Méndez
- Instituto de Investigaciones Marinas (IIM-CSIC), Vigo, Spain.
| | - Isabel Medina
- Instituto de Investigaciones Marinas (IIM-CSIC), Vigo, Spain.
| | - Núria Taltavull
- Faculty of Medicine and Health Science, Universitat Rovira i Virgili, Reus, Spain.
| | - Marta Romeu
- Faculty of Medicine and Health Science, Universitat Rovira i Virgili, Reus, Spain.
| | - Maria Rosa Nogués
- Faculty of Medicine and Health Science, Universitat Rovira i Virgili, Reus, Spain.
| | - Josep Lluís Torres
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona, Spain.
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Yasmin R, Zhu H, Chen Z, Montagna RA. A modifiable microarray-based universal sensor: providing sample-to-results automation. Heliyon 2016; 2:e00179. [PMID: 27812551 PMCID: PMC5078625 DOI: 10.1016/j.heliyon.2016.e00179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/22/2016] [Accepted: 10/11/2016] [Indexed: 12/30/2022] Open
Abstract
A microfluidic system consisting of generic single use cartridges which interface with a workstation allows the automatic performance of all necessary sample preparation, PCR analysis and interpretation of multiplex PCR assays. The cartridges contain a DNA array with 20 different 16mer DNA “universal” probes immobilized at defined locations. PCR amplicons can be detected via hybridization of user-defined “reporter” probes that are complementary at their 3′ termini to one or more of the universal probes and complementary to the target amplicons at their 5′ termini. The system was able to detect single-plex and multiplex PCR amplicons from various infectious agents as well as wild type and mutant alleles of single nucleotide polymorphisms. The system's ease of use was further demonstrated by converting a published PCR assay for the detection of Mycobacterium genitalium in a fully automated manner. Excellent correlation between traditional manual methods and the automated analysis performed by the workstation suggests that the system can provide a means to easily design and implement a variety of customized PCR-based assays. The system will be useful to researchers or clinical investigators seeking to develop their own user defined assays. As the U.S. FDA continues to pursue regulatory oversight of LDTs, the system would also allow labs to continue to develop compliant assays.
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Affiliation(s)
| | - Hui Zhu
- Rheonix Inc., 10 Brown Road, Ithaca, NY 14850, USA
| | - Zongyuan Chen
- Rheonix Inc., 10 Brown Road, Ithaca, NY 14850, USA; Thermo Fisher Scientific, South San Francisco, CA, USA
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Park S, Cui F, Mo K, Kim M. Mathematical models and bacterial communities for ammonia toxicity in mesophilic anaerobes not acclimated to high concentrations of ammonia. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2016; 74:935-942. [PMID: 27533868 DOI: 10.2166/wst.2016.274] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In this study, we evaluated ammonia toxicity in mesophilic anaerobic digestion at various pH values and total ammonia nitrogen (TAN) concentrations. We performed anaerobic toxicity assays (ATAs) to evaluate the toxicity effects of TAN and pH on mesophilic anaerobic digestion. Modeling based on the results of the ATAs indicated that the specific methanogenic activity (SMA) decreased by 30% at a TAN concentration higher than 3.0 g/L compared to a TAN concentration of 0 g/L. In addition, the highest SMA for a given TAN level (0.5-10.0 g/L) was observed at a pH of around 7.6. The results of bacterial community analyses showed that the diversity and richness of microorganisms with increasing TAN concentration were decreased. Chloroflexi and Synergistetes were the dominant phyla at TAN concentrations less than 3.0 g/L, and Firmicutes was the dominant phylum at TAN concentrations higher than 3.0 g/L, implying that the ammonia toxicity concentration may influence the kind of dominant species. In conclusion, to start a stable mesophilic anaerobic digestion concerning ammonia toxicity, a TAN concentration less than 3.0 g/L is preferable.
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Affiliation(s)
- Seyong Park
- Plant Engineering Center, Institute for Advanced Engineering, 51 Goan-ro, Yongin City, Kyeonggido 175-28, Republic of Korea; Department of Civil & Environmental Engineering, Hanyang University, 55 Hanyangdaehak-ro, Ansan City, Kyeonggido 155-88, Republic of Korea E-mail:
| | - Fenghao Cui
- Department of Civil & Environmental Engineering, Hanyang University, 55 Hanyangdaehak-ro, Ansan City, Kyeonggido 155-88, Republic of Korea E-mail:
| | - Kyung Mo
- Department of Civil & Environmental Engineering, Hanyang University, 55 Hanyangdaehak-ro, Ansan City, Kyeonggido 155-88, Republic of Korea E-mail:
| | - Moonil Kim
- Department of Civil & Environmental Engineering, Hanyang University, 55 Hanyangdaehak-ro, Ansan City, Kyeonggido 155-88, Republic of Korea E-mail:
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Zhang Y, Tao Y, Zhang H, Wang L, Sun G, Sun X, Erinle KO, Feng C, Song Q, Li M. Effect of di-n-butyl phthalate on root physiology and rhizosphere microbial community of cucumber seedlings. JOURNAL OF HAZARDOUS MATERIALS 2015; 289:9-17. [PMID: 25702635 DOI: 10.1016/j.jhazmat.2015.01.071] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/24/2015] [Accepted: 01/28/2015] [Indexed: 05/20/2023]
Abstract
The authors investigated the effects of di-n-butyl phthalate (DBP) on root physiology and rhizosphere microbial communities of cucumber seedlings (sativus L. cv Jinyan No. 4). Root protein content and root activity were observed to decrease. From the ultrastructural micrographs, visible impact on the mitochondria, endoplasmic reticulum and vacuole were detected. Moreover, the number of starch grains increased, and some were adhered to other cell components which might be the most direct evidence of DBP causing cellular damage. Results of PCR-DGGE (denaturing gradient gel electrophoresis) indicated that DBP significantly changed the abundance, structure and composition of rhizosphere bacteria when the concentration was higher than 50 mg L(-1). The relative abundances of Firmicutes increased while that of Bacteroidetes decreased. Bacillus was detected as the dominant bacteria in DBP contaminated cucumber rhizospheric soil. The amount of Actinobacteridae and Pseudomonas decreased until it disappeared in the rhizosphere soil when exposed to DBP concentrations higher than 50 mg L(-1).
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Affiliation(s)
- Ying Zhang
- School of Resources & Environment, Northeast Agricultural University, Harbin 150030, PR China.
| | - Yue Tao
- School of Resources & Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Hui Zhang
- School of Resources & Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Lei Wang
- School of Resources & Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Guoqiang Sun
- School of Resources & Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Xin Sun
- School of Resources & Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Kehinde O Erinle
- School of Resources & Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Chengcheng Feng
- School of Resources & Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Qiuxia Song
- School of Resources & Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Mo Li
- School of Geography, University of Nottingham, Nottinghamshire NG72RD, UK
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Wieme AD, Spitaels F, Aerts M, De Bruyne K, Van Landschoot A, Vandamme P. Identification of beer-spoilage bacteria using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Int J Food Microbiol 2014; 185:41-50. [PMID: 24929682 DOI: 10.1016/j.ijfoodmicro.2014.05.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 04/22/2014] [Accepted: 05/04/2014] [Indexed: 11/26/2022]
Abstract
Applicability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for identification of beer-spoilage bacteria was examined. To achieve this, an extensive identification database was constructed comprising more than 4200 mass spectra, including biological and technical replicates derived from 273 acetic acid bacteria (AAB) and lactic acid bacteria (LAB), covering a total of 52 species, grown on at least three growth media. Sequence analysis of protein coding genes was used to verify aberrant MALDI-TOF MS identification results and confirmed the earlier misidentification of 34 AAB and LAB strains. In total, 348 isolates were collected from culture media inoculated with 14 spoiled beer and brewery samples. Peak-based numerical analysis of MALDI-TOF MS spectra allowed a straightforward species identification of 327 (94.0%) isolates. The remaining isolates clustered separately and were assigned through sequence analysis of protein coding genes either to species not known as beer-spoilage bacteria, and thus not present in the database, or to novel AAB species. An alternative, classifier-based approach for the identification of spoilage bacteria was evaluated by combining the identification results obtained through peak-based cluster analysis and sequence analysis of protein coding genes as a standard. In total, 263 out of 348 isolates (75.6%) were correctly identified at species level and 24 isolates (6.9%) were misidentified. In addition, the identification results of 50 isolates (14.4%) were considered unreliable, and 11 isolates (3.2%) could not be identified. The present study demonstrated that MALDI-TOF MS is well-suited for the rapid, high-throughput and accurate identification of bacteria isolated from spoiled beer and brewery samples, which makes the technique appropriate for routine microbial quality control in the brewing industry.
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Affiliation(s)
- Anneleen D Wieme
- Laboratory of Biochemistry and Brewing, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, B-9000 Ghent, Belgium; Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Freek Spitaels
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Maarten Aerts
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Katrien De Bruyne
- Applied Maths N.V., Keistraat 120, B-9830 Sint-Martens-Latem, Belgium
| | - Anita Van Landschoot
- Laboratory of Biochemistry and Brewing, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, B-9000 Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
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Extensive host range determination and improved efficacy of the bacteriophage JBP901 in the presence of divalent cations for control of Bacillus cereus in Cheonggukjang. Food Sci Biotechnol 2014. [DOI: 10.1007/s10068-014-0068-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Deng Y, Liu J, Li H, Li L, Tu J, Fang H, Chen J, Qian F. An improved plate culture procedure for the rapid detection of beer-spoilage lactic acid bacteria. JOURNAL OF THE INSTITUTE OF BREWING 2014. [DOI: 10.1002/jib.121] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yang Deng
- College of Light Industry and Food Sciences; South China University of Technology; Guangzhou 510640 People's Republic of China
- Technical Center; Zhujiang Brewery Co. Ltd; No. 118, Modiesha Avenue, East Xingang Road Guangzhou 510308 People's Republic of China
| | - Junyan Liu
- College of Light Industry and Food Sciences; South China University of Technology; Guangzhou 510640 People's Republic of China
| | - Huiping Li
- Technical Center; Zhujiang Brewery Co. Ltd; No. 118, Modiesha Avenue, East Xingang Road Guangzhou 510308 People's Republic of China
| | - Lin Li
- College of Light Industry and Food Sciences; South China University of Technology; Guangzhou 510640 People's Republic of China
| | - Jingxia Tu
- Technical Center; Zhujiang Brewery Co. Ltd; No. 118, Modiesha Avenue, East Xingang Road Guangzhou 510308 People's Republic of China
| | - Huijing Fang
- Technical Center; Zhujiang Brewery Co. Ltd; No. 118, Modiesha Avenue, East Xingang Road Guangzhou 510308 People's Republic of China
| | - Jiang Chen
- Technical Center; Zhujiang Brewery Co. Ltd; No. 118, Modiesha Avenue, East Xingang Road Guangzhou 510308 People's Republic of China
| | - Fei Qian
- Institute of Brewing and Beverage Technology; Centre of Life and Food Sciences, TUM; Germany
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Hermann-Bank ML, Skovgaard K, Stockmarr A, Larsen N, Mølbak L. The Gut Microbiotassay: a high-throughput qPCR approach combinable with next generation sequencing to study gut microbial diversity. BMC Genomics 2013; 14:788. [PMID: 24225361 PMCID: PMC3879714 DOI: 10.1186/1471-2164-14-788] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 10/14/2013] [Indexed: 12/12/2022] Open
Abstract
Background The intestinal microbiota is a complex and diverse ecosystem that plays a significant role in maintaining the health and well-being of the mammalian host. During the last decade focus has increased on the importance of intestinal bacteria. Several molecular methods can be applied to describe the composition of the microbiota. This study used a new approach, the Gut Microbiotassay: an assembly of 24 primer sets targeting the main phyla and taxonomically related subgroups of the intestinal microbiota, to be used with the high-throughput qPCR chip ‘Access Array 48.48′, AA48.48, (Fluidigm®) followed by next generation sequencing. Primers were designed if necessary and all primer sets were screened against DNA extracted from pure cultures of 15 representative bacterial species. Subsequently the setup was tested on DNA extracted from small and large intestinal content from piglets with and without diarrhoea. The PCR amplicons from the 2304 reaction chambers were harvested from the AA48.48, purified, and sequenced using 454-technology. Results The Gut Microbiotassay was able to detect significant differences in the quantity and composition of the microbiota according to gut sections and diarrhoeic status. 454-sequencing confirmed the specificity of the primer sets. Diarrhoea was associated with a reduced number of members from the genus Streptococcus, and in particular S. alactolyticus. Conclusion The Gut Microbiotassay provides fast and affordable high-throughput quantification of the bacterial composition in many samples and enables further descriptive taxonomic information if combined with 454-sequencing.
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Affiliation(s)
| | | | | | | | - Lars Mølbak
- Present address: Chr, Hansen, Bøge Allé 10, 2970 Hørsholm, Denmark.
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Lee JE, Lee S, Lee H, Song YM, Lee K, Han MJ, Sung J, Ko G. Association of the vaginal microbiota with human papillomavirus infection in a Korean twin cohort. PLoS One 2013; 8:e63514. [PMID: 23717441 PMCID: PMC3661536 DOI: 10.1371/journal.pone.0063514] [Citation(s) in RCA: 210] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 04/03/2013] [Indexed: 01/21/2023] Open
Abstract
Human papillomavirus (HPV) is the most important causative agent of cervical cancers worldwide. However, our understanding of how the vaginal microbiota might be associated with HPV infection is limited. In addition, the influence of human genetic and physiological factors on the vaginal microbiota is unclear. Studies on twins and their families provide the ideal settings to investigate the complicated nature of human microbiota. This study investigated the vaginal microbiota of 68 HPV-infected or uninfected female twins and their families using 454-pyrosequencing analysis targeting the variable region (V2–V3) of the bacterial 16S rRNA gene. Analysis of the vaginal microbiota from both premenopausal women and HPV-discordant twins indicated that HPV-positive women had significantly higher microbial diversity with a lower proportion of Lactobacillus spp. than HPV-negative women. Fusobacteria, including Sneathia spp., were identified as a possible microbiological marker associated with HPV infection. The vaginal microbiotas of twin pairs were significantly more similar to each other than to those from unrelated individuals. In addition, there were marked significant differences from those of their mother, possibly due to differences in menopausal status. Postmenopausal women had a lower proportion of Lactobacillus spp. and a significantly higher microbiota diversity. This study indicated that HPV infection was associated with the composition of the vaginal microbiota, which is influenced by multiple host factors such as genetics and menopause. The potential biological markers identified in this study could provide insight into HPV pathogenesis and may represent biological targets for diagnostics.
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Affiliation(s)
- Jung Eun Lee
- Department of Environmental Health and Institute of Health and Environment, School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Sunghee Lee
- Department of Environmental Health and Institute of Health and Environment, School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Heetae Lee
- Department of Environmental Health and Institute of Health and Environment, School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Yun-Mi Song
- Department of Family Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kayoung Lee
- Department of Family Medicine, Busan Paik Hospital, Inje University College of Medicine, Busan, Republic of Korea
| | - Min Ji Han
- Department of Epidemiology, School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Joohon Sung
- Department of Epidemiology, School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - GwangPyo Ko
- Department of Environmental Health and Institute of Health and Environment, School of Public Health, Seoul National University, Seoul, Republic of Korea
- * E-mail:
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Shillitoe E, Weinstock R, Kim T, Simon H, Planer J, Noonan S, Cooney R. The oral microflora in obesity and type-2 diabetes. J Oral Microbiol 2012; 4:19013. [PMID: 23119124 PMCID: PMC3485401 DOI: 10.3402/jom.v4i0.19013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 09/13/2012] [Accepted: 10/01/2012] [Indexed: 12/28/2022] Open
Abstract
Background Type 2 diabetes mellitus (T2DM) is prevalent in people with obesity. It has been proposed that these conditions are related to specific features of the microflora of the mouth and lower gastrointestinal (GI) tract. Hyperglycemia often resolves quickly after Roux-en-Y gastric bypass (RYGB) but the role of the GI microflora cannot be examined easily because of reduced intestinal mobility. We propose that the study of microorganisms present in the mouth of patients undergoing RYGB will contribute to our understanding of the role of bacteria in the pathogenesis of T2DM. Objective To conduct a feasibility study to examine differences in oral microbes in obese patients with and without T2DM and to determine whether it is feasible to measure changes after gastric bypass surgery. Methods Individuals with morbid obesity (n=29), of whom 13 had T2DM, were studied. Oral rinses, stool samples, and blood samples were obtained before RYGB, and oral rinses and blood samples were obtained at 2 and 12 weeks postsurgery. Results Prior to surgery, participants with T2DM had slightly higher total levels of oral bacteria than those without diabetes. Those with HbA1c > 6.5% had rather lower levels of Bifidobacteria in the mouth and stool. At 2 weeks post-RYGB, patients with T2DM were able to reduce or discontinue their hypoglycemic medications. Stool samples could not be obtained but oral rinses were readily available. The levels of oral Bifidobacteria had increased tenfold and levels of circulating endotoxin and tumor necrosis factor-alpha had decreased. Conclusions The study of oral bacteria before and after RYGB is feasible and should be tested in larger patient populations to increase our understanding of the role of microorganisms in the pathogenesis of obesity and T2DM.
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Affiliation(s)
- Edward Shillitoe
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY, USA
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Khemkhao M, Nuntakumjorn B, Techkarnjanaruk S, Phalakornkule C. UASB performance and microbial adaptation during a transition from mesophilic to thermophilic treatment of palm oil mill effluent. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2012; 103:74-82. [PMID: 22466006 DOI: 10.1016/j.jenvman.2012.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Revised: 02/16/2012] [Accepted: 03/02/2012] [Indexed: 05/31/2023]
Abstract
The treatment of palm oil mill effluent (POME) by an upflow anaerobic sludge bed (UASB) at organic loading rates (OLR) between 2.2 and 9.5 g COD l(-1) day(-1) was achieved by acclimatizing the mesophilic (37 °C) microbial seed to the thermophilic temperature (57 °C) by a series of stepwise temperature shifts. The UASB produced up to 13.2 l biogas d(-1) with methane content on an average of 76%. The COD removal efficiency ranged between 76 and 86%. Microbial diversity of granules from the UASB reactor was also investigated. The PCR-based DGGE analysis showed that the bacterial population profiles significantly changed with the temperature transition from mesophilic to thermophilic conditions. In addition, the results suggested that even though the thermophilic temperature of 57 °C was suitable for a number of hydrolytic, acidogenic and acetogenic bacteria, it may not be suitable for some Methanosaeta species acclimatized from 37 °C. Specifically, the bands associated with Methanosaeta thermophila PT and Methanosaeta harundinacea can be detected during the four consecutive operation phases of 37 °C, 42 °C, 47 °C and 52 °C, but their corresponding bands were found to fade out at 57 °C. The DGGE analysis predicted that the temperature transition can result in significant methanogenic biomass washout at 57 °C.
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Affiliation(s)
- Maneerat Khemkhao
- Joint Graduate School of Energy and Environment, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
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Ji YS, Kim HN, Park HJ, Lee JE, Yeo SY, Yang JS, Park SY, Yoon HS, Cho GS, Franz CMAP, Bomba A, Shin HK, Holzapfel WH. Modulation of the murine microbiome with a concomitant anti-obesity effect by Lactobacillus rhamnosus GG and Lactobacillus sakei NR28. Benef Microbes 2012; 3:13-22. [PMID: 22348905 DOI: 10.3920/bm2011.0046] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The microbiota of the gastrointestinal tract (GIT) constitutes the major part of the total human microbiome and is considered to be an important regulator of human health and host metabolism. Numerous investigations in recent years have focused on the connection between the human microbiota and metabolic diseases such as obesity, type II diabetes and atherosclerosis. Yet, little is known about the impact of probiotic consumption on the GIT microbial population and the potential effect on chronic diseases. In this study, the modulation of the microbial community in the murine small intestine resulting from probiotic feeding was investigated and was found to be associated with an anti-obesity effect. Changes in the microbiota of the mouse faeces and small intestine were monitored using quantitative real-time PCR and by following the mRNA expression levels of various obesity-related biomarkers following probiotic feeding in a mouse model. Lactobacillus rhamnosus GG and Lactobacillus sakei NR28 (a putative probiotic strain isolated from kimchi) were administered at a daily level of approximately 1×10(8) viable bacteria per mouse (C57BL/6J mice) for up to three weeks. Feeding these strains resulted in a significant reduction of epididymal fat mass, as well as obesity-related biomarkers like acetyl-CoA carboxylase, fatty acid synthase, and stearoyl-CoA desaturase-1 in the liver. The total number and ratio of the microbial groups, i.e. Firmicutes, Bacteroidetes, Clostridium cluster I and XIVab, and Lactobacillus spp. were modulated in the small intestine, and the Firmicutes:Bacteroidetes ratio was decreased. In contrast, no noticeable effect of probiotic feeding could be detected on the faecal microbiota, neither quantitatively, nor with regard to the bacterial groups (Firmicutes, Bacteroidetes, Clostridium cluster I and XIVab, and Lactobacillus spp.) studied.
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Affiliation(s)
- Y S Ji
- School of Life Science, Handong Global University, Pohang, Gyungbuk, Republic of Korea
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Taskila S, Neubauer P, Tuomola M, Breitenstein A, Kronlöf J, Hillukkala T. Improved Enrichment Cultivation of Beer Spoiling Lactic Acid Bacteria by Continuous Glucose Addition to the Culture. JOURNAL OF THE INSTITUTE OF BREWING 2012. [DOI: 10.1002/j.2050-0416.2009.tb00366.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Taskila S, Kronlöf J, Ojamo H. Enrichment Cultivation of Beer-Spoiling Lactic Acid Bacteria. JOURNAL OF THE INSTITUTE OF BREWING 2012. [DOI: 10.1002/j.2050-0416.2011.tb00473.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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qPCR as a powerful tool for microbial food spoilage quantification: Significance for food quality. Trends Food Sci Technol 2011. [DOI: 10.1016/j.tifs.2011.04.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Principi P, Villa F, Sorlini C, Cappitelli F. Molecular studies of microbial community structure on stained pages of Leonardo da Vinci's Atlantic Codex. MICROBIAL ECOLOGY 2011; 61:214-222. [PMID: 20811884 DOI: 10.1007/s00248-010-9741-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 08/16/2010] [Indexed: 05/29/2023]
Abstract
In 2006, after a visual inspection of the Leonardo da Vinci's Atlantic Codex by a scholar, active molds were reported to have been present on Codex pages showing areas of staining. In the present paper, molecular methods were used to assess the current microbiological risk to stained pages of the manuscript. Bacterial and fungal communities were sampled by a non-invasive technique employing nitrocellulose membranes. Denaturing gradient gel electrophoresis of 16 S rRNA gene and internal transcribed space regions were carried out to study the structure of the bacterial and fungal communities and band patterns were analyzed by the multivariate technique of principal component analysis. Any relationship between the presence of an active microbial community and staining was excluded. The presence of potential biodeteriogens was evaluated by constructing bacterial and fungal clone libraries, analyzing them by an operational taxonomic unit (OTU) approach. Among the bacteria, some OTUs were associated with species found on floors in clean room while others were identified with human skin contamination. Some fungal OTU representatives were potential biodeteriogens that, under proper thermo-hygrometric conditions, could grow. The retrieval of these potential biodeteriogens and microorganisms related to human skin suggests the need for a continuous and rigorous monitoring of the environmental conditions, and the need to improve handling procedures.
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Affiliation(s)
- Pamela Principi
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche (DiSTAM), Università degli Studi di Milano, via Celoria 2, 20133, Milan, Italy
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Trost B, Haakensen M, Pittet V, Ziola B, Kusalik A. Analysis and comparison of the pan-genomic properties of sixteen well-characterized bacterial genera. BMC Microbiol 2010; 10:258. [PMID: 20942950 PMCID: PMC3020658 DOI: 10.1186/1471-2180-10-258] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 10/13/2010] [Indexed: 11/10/2022] Open
Abstract
Background The increasing availability of whole genome sequences allows the gene or protein content of different organisms to be compared, leading to burgeoning interest in the relatively new subfield of pan-genomics. However, while several studies have analyzed protein content relationships in specific groups of bacteria, there has yet to be a study that provides a general characterization of protein content relationships in a broad range of bacteria. Results A variation on reciprocal BLAST hits was used to infer relationships among proteins in several groups of bacteria, and data regarding protein conservation and uniqueness in different bacterial genera are reported in terms of "core proteomes", "unique proteomes", and "singlets". We also analyzed the relationship between protein content similarity and the percent identity of the 16S rRNA gene in pairs of bacterial isolates from the same genus, and found that the strength of this relationship varied substantially depending on the genus, perhaps reflecting different rates of genome evolution and/or horizontal gene transfer. Finally, core proteomes and unique proteomes were used to study the proteomic cohesiveness of several bacterial species, revealing that some bacterial species had little cohesiveness in their protein content, with some having fewer proteins unique to that species than randomly-chosen sets of isolates from the same genus. Conclusions The results described in this study aid our understanding of protein content relationships in different bacterial groups, allowing us to make further inferences regarding genome-environment relationships, genome evolution, and the soundness of existing taxonomic classifications.
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Affiliation(s)
- Brett Trost
- Department of Computer Science, University of Saskatchewan, 176 Thorvaldson Building, 110 Science Place, Saskatoon, Saskatchewan, S7N 5C9, Canada.
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